pibase | pibase step 1 | pibase_bamref example: 1000 Genomes NA12878 SOLiD chr22




The tab-separated text file (above, and in full detail below) shows example output from pibase_bamref. The header lines all start with '#' so that they can be grep'd away from the linux command line or easily parsed with scripts.

Columns 1 and 2 are the genomic coordinates of interest (chromosome number, and 1-based position in chromosome.
Columns 3, 4, and 5 are as extracted from the reference sequence: reference base, window of 13 bases, GC-content in this window. Column 6 denotes whether homopolymeric runs or STRs occur.

Column 7 reports how many reads in the BAM file at the genomic coordinate of interest were ignored due to indels-in-a-read or data conflicts in the BAM-file.

The remaining columns are counts of reads which support each nucleotide (A, C, G, T, or N, on each strand), for 10 different criteria: There are 5 filter levels. Within each filter level there are unique-start-point counts and coverage counts. The most stringent filter level is the leftmost group and the least stringent level is the rightmost group:

The rightmost group is unfiltered. (The coverage counts correspond to those in a genome viewer).
The next group applies a PHRED-like base quality filter (user-specifiable, default=20) so that sequencing errors are eliminated.
The next group additionally applies a mapped-read-length filter (user-specifiable, default=49) to filter shortened reads which were mapped by the aligner, because genomic lower complexity loci may lead to alignment of read fragments from other genomic loci.
The next group additionally applies a maximal mismatch filter (user-specifiable, default=1) to filter reads with multiple mismatches, because on average in the human genome there is only about 1 mismatch in 1000 nucleotides.
The leftmost group additionally applies a minimal mapping quality filter (user-specifiable, default=20) so that multiple-mappable reads or otherwise poorly mapped reads are eliminated.

# Position Info (1-based coordinates) generated by pibase_bamref v1.4 from file NA12878.chrom22.SOLID.bfast.CEU.high_coverage.20100125.bam
# Reference: hg19.1000G.quick.fasta
# Positions of interest taken from file: hg19_chr22_genomic_coords_of_interest.txt
# Max fragment length considered: 50 bases
# Base quality value threshold QVmin= 20
# Mapped-length-of-read threshold MLmin= 34 bases
# Mismatch-in-read threshold MMmax= 1
# Read-mapping quality value threshold RQVmin= 20
# Column "Ign" denotes number of ignored reads due to indels (usually bad mapping!)
# Column "RefSeqcontext" denotes the poi-Refbase and the +-6 Refbases
# Column "Class" denotes context class (e.g. stretches or STRs)
# Date: 2011_10_28__15:19:27

# 							MapQV>RQVmin and MM<=MMmax and Read>MLmin and BaseQVs>=QVmin															MM<=MMmax and Read>MLmin and BaseQVs>=QVmin															Read>MLmin and BaseQVs>=QVmin																	BaseQVs>=QVmin																			No QV-Filtering
# 							Unique start points (on +- strands)								Coverage									Unique start points (on +- strands)						Coverage									Unique start points (on +- strands)						Coverage									Unique start points (on +- strands)						Coverage									Unique start points (on +- strands)						Coverage									
# C	Pos[1]		Ref	RefSeqContext	GC[%]	Class	Ign	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-	A+	A-	C+	C-	G+	G-	T+	T-	N+	N-
22	17662444	C	TTTTCT[C]ACTCTC	38	5	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	3	1	0	0	0	0	0	0	0	0	3	1	0	0	0	0	0	0	0	0	5	2	0	0	0	0	0	0	0	0	5	2	0	0	0	0	0	0
22	17662793	A	GAAATC[A]TAGGAC	38	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0
22	17669306	T	TAGTCA[T]GCAAGG	46	1	1	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	2	4	0	0	0	0	0	0	0	0	2	4	0	0	0	0	0	0	0	0	2	5	0	0	0	0	0	0	0	0	2	5	0	0
22	19958811	C	CCTGAC[C]GCGGGC	84	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0
22	19958829	G	GGGCCC[G]GGGGGA	92	9	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0
22	19968971	G	GGGCCT[G]GGCCAA	76	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0
22	19969075	A	ACCCCC[A]CTGCTG	69	8	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0
22	19969106	A	GTGGCC[A]CTGGGC	76	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
22	19969495	G	GGATGT[G]ACAATA	38	1	3	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	2	4	0	0	0	0	0	0	0	0	3	5	0	0	0	0	0	0	0	0	4	4	0	0	0	0	0	0	0	0	6	5	0	0	0	0
22	22318538	C	CCGTGT[C]GGCCCA	76	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
22	22318671	G	CATGGC[G]TGCTGC	69	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0
22	23503121	G	GCAGTC[G]GTGCTG	69	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	1	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0
22	23503170	A	GTCGGC[A]ATGGAG	61	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
22	24579503	T	GACTCC[T]CCGGGC	76	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0
22	24582041	A	CATTCA[A]TGGGCG	53	1	1	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	6	4	0	0	0	0	0	0	0	0	6	4	0	0	0	0	0	0	0	0	7	4	0	0	0	0	0	0	0	0	7	4	0	0	0	0	0	0	0	0
22	30823196	T	GGTGAC[T]GTGGCT	61	1	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0
22	30823250	G	CATTCC[G]GGCTTC	61	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0
22	30856121	G	CGAAGC[G]TAGGAC	61	1	4	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	2	4	0	0	0	0	0	0	0	0	2	5	0	0	0	0
22	30857373	A	TAGAAC[A]TCTGTC	38	1	3	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	1	1	1	0	0	0	0	0	0	2	1	1	1	0	0	0	0	0	0
22	30857448	A	CGCACC[A]TCAGAT	53	1	2	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	0	0	3	3	0	0	0	0	0	0	0	0	3	3	0	0	0	0	0	0	0	0	3	4	0	0	0	0	0	0	0	0
22	30860830	C	TTCCTG[C]GAGTGT	53	1	2	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	2	4	0	0	0	0	0	0
22	30864610	A	GGCCCA[A]TGATGT	53	1	3	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0
22	30864627	G	CCACAC[G]GGGCAG	76	4	2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	3	3	0	0	0	0	0	0	0	0	4	3	0	0	0	0
22	30951948	G	GGTGCT[G]CTGGCC	76	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	4	3	0	0	0	0	0	0	0	0	4	4	0	0	0	0
22	30953280	C	GGGGCA[C]GGCATA	69	4	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
22	30953295	C	AGTACA[C]CAGCAG	53	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0
22	31487701	C	ACTCAG[C]ACCAGT	53	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0
22	31491295	G	ATGGAA[G]CAGAGC	53	1	10	0	0	1	0	0	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	2	0	0	1	0	0	0	0	0	0	2	0	0	1	0	0	0	0	0	0	2	0	1	1	0	0	0	0	0	0	2	0	1	1	0	0	0	0	0	0	2	0	4	1	0	0	0	0	0	0	2	0	4	1	0	0	0	0
22	31491332	C	TGGAAG[C]GGCCAA	61	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
22	31655196	G	ACTGGT[G]CAGCAT	53	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0	0	0
22	31658205	C	CCCGTC[C]GCACAC	76	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	2	4	0	0	0	0	0	0
22	31663842	C	GAACCT[C]CTGACA	53	1	4	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	1	3	0	0	0	0	0	0	0	3	2	3	0	0	0	0	0	0	0	3	2	3	0	0	0	0
22	33670584	G	GTAGGC[G]TTGGGC	69	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	4	0	0	0	0
22	33673125	C	CAGTCA[C]GTCTCA	53	1	2	0	0	2	2	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	0	0	2	3	0	0	1	0	0	0	0	0	3	3	0	0	1	0	0	0
22	34000460	G	CACAGC[G]GGCACC	76	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	1	0	0	0	0	0	0	0	0	7	1	0	0	0	0
22	34000484	C	GAAGAG[C]GTGGCC	69	1	6	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	5	2	0	0	0	0	0	0	0	0	5	2	0	0	0	0	0	0
22	34022284	G	GTATCC[G]GCGCAG	69	1	2	0	3	0	0	0	1	0	0	0	0	0	3	0	0	0	1	0	0	0	0	0	3	0	0	0	1	0	0	0	0	0	3	0	0	0	1	0	0	0	0	1	3	0	0	0	1	0	0	0	0	1	3	0	0	0	1	0	0	0	0	1	4	0	0	0	1	0	0	0	0	1	4	0	0	0	1	0	0	0	0	1	4	0	0	2	1	0	0	0	0	1	4	0	0	2	1	0	0	0	0
22	39095987	A	CACACA[A]CTCATG	46	500	2	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	3	5	0	0	0	0	0	0	0	0	3	5	0	0	0	0	0	0	0	0
22	39440149	C	AGTGCG[C]CCCACC	76	3	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	0	0	1	0	0	0	0	1	2	0	0	0	1	0	0
22	39627630	G	CACCTG[G]ACAGGT	61	1	3	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0
22	40283427	A	TCATCT[A]TGTGCT	38	1	1	2	1	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	2	3	0	0	1	0	0	0	0	0	2	3	0	0	1	0	0	0	0	0	2	4	0	0	1	0	0	0	0	0	2	4	0	0	1	0	0	0	0	0
22	40417495	C	CAAGTA[C]GCCTTG	53	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0
22	40417571	G	GCGGGC[G]GCAACC	84	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0
22	40417780	C	CCGAAA[C]GGCATG	61	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
22	40417820	A	CCCGCC[A]GGCGCT	84	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0
22	40417943	G	CCCAAC[G]AGAATT	46	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	2	5	0	0	0	0	0	0	0	0	3	5	0	0	0	0
22	45312244	G	GGCGGC[G]GCATTG	76	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0
22	45312345	C	GGCTGC[C]GGGCGC	92	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
22	50616806	A	TGGGCT[A]GGCCTG	69	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0
22	21998280	G	CTGTGC[G]CTTCCA	61	1	4	1	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	1	1	0	0	0	0	1	1	0	0	1	1	0	0	0	0	1	1	0	0	3	1	0	0	0	0	1	1	0	0	3	1	0	0	0	0
22	22318354	T	GCGTCA[T]GGCCTT	61	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	1	0	0	0	2	2	0	0	0	0	1	0	0	0	2	2	0	0	0	0	1	0	0	0	2	2	0	0	0	0	1	0	0	0	2	2	0	0
22	24580807	C	CAACTC[C]GGCTCT	61	1	2	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	4	1	0	0	0	0	0	0	0	0	5	1	0	0	0	0	0	0
22	24580897	C	AAATTA[C]GCAGGG	46	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	3	4	0	0	0	0	0	0	0	0	3	4	0	0	0	0	0	0
22	45279003	G	GGGTGT[G]TGGCTG	69	1000	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0



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