BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1708563.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 4,240,877
number of mapped reads = 3,502,636 (82.59%)
number of supplementary alignments = 115 (0%)
number of secondary alignments = 0
number of mapped bases = 174,612,960 bp
number of sequenced bases = 174,597,452 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 125,786
duplication rate = 3.51%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 41.752
>>>>>>> ACTG content
number of A's = 53,918,380 bp (30.88%)
number of C's = 33,368,163 bp (19.11%)
number of T's = 53,517,948 bp (30.65%)
number of G's = 33,785,894 bp (19.35%)
number of N's = 7,067 bp (0%)
GC percentage = 38.46%
>>>>>>> Mismatches and indels
general error rate = 0.0017
number of mismatches = 278,920
number of insertions = 13,052
mapped reads with insertion percentage = 0.37%
number of deletions = 9,157
mapped reads with deletion percentage = 0.26%
homopolymer indels = 48.35%
>>>>>>> Coverage
mean coverageData = 0.0564X
std coverageData = 0.4875X
There is a 2.86% of reference with a coverageData >= 1X
There is a 0.99% of reference with a coverageData >= 2X
There is a 0.56% of reference with a coverageData >= 3X
There is a 0.36% of reference with a coverageData >= 4X
There is a 0.24% of reference with a coverageData >= 5X
There is a 0.17% of reference with a coverageData >= 6X
There is a 0.12% of reference with a coverageData >= 7X
There is a 0.09% of reference with a coverageData >= 8X
There is a 0.06% of reference with a coverageData >= 9X
There is a 0.05% of reference with a coverageData >= 10X
There is a 0.04% of reference with a coverageData >= 11X
There is a 0.03% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.02% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 28820909 0.11563023949296398 0.7547594854065731
chr2 243199373 6864802 0.028227054680770084 0.33019232030428103
chr3 198022430 16417160 0.08290555771889073 0.541903835660485
chr4 191154276 12702157 0.0664497664703038 0.5447589844103718
chr5 180915260 5523055 0.03052840871466564 0.2760412206490574
chr6 171115067 19533744 0.11415560501168491 0.7722455981816434
chr7 159138663 7926662 0.049809781297458805 0.4058893551402232
chr8 146364022 7085531 0.04841033269774453 0.5187247223688956
chr9 141213431 4929634 0.0349091015287349 0.26926433240174086
chr10 135534747 1834108 0.013532382216347812 0.15492691807623785
chr11 135006516 6070287 0.044962918678680665 0.4372869709679431
chr12 133851895 9768863 0.07298262755263943 0.5327073374227789
chr13 115169878 3482244 0.030235718405467096 0.32492053825587797
chr14 107349540 8479600 0.0789905573885086 0.579826816978355
chr15 102531392 1546634 0.015084492366981617 0.2106489964517989
chr16 90354753 10067397 0.11142077938058223 0.6700968575445432
chr17 81195210 5498238 0.06771628523406738 0.6290531483047379
chr18 78077248 1012132 0.012963213047672992 0.12881142676537244
chr19 59128983 2738681 0.04631706586260751 0.32550878851885806
chr20 63025520 4085354 0.06482063138868192 0.48674124160944005
chr21 48129895 2532895 0.052626231576029824 0.5407756430956667
chr22 51304566 3220050 0.06276341953657692 0.4594459595968155
chrMT 16571 0 0.0 0.0
chrX 155270560 4332892 0.027905431654268523 0.33146473201627435
chrY 59373566 139931 0.0023567895517678694 0.05315103792894039