BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549046.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 2,832,202 number of mapped reads = 2,084,744 (73.61%) number of secondary alignments = 0 number of mapped bases = 82,526,268 bp number of sequenced bases = 82,518,532 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,433 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6119 >>>>>>> ACTG content number of A's = 23,501,558 bp (28.48%) number of C's = 17,265,478 bp (20.92%) number of T's = 24,246,813 bp (29.38%) number of G's = 17,504,041 bp (21.21%) number of N's = 642 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 198,541 number of insertions = 2,347 mapped reads with insertion percentage = 0.11% number of deletions = 5,866 mapped reads with deletion percentage = 0.28% homopolymer indels = 41.85% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 0.2338X There is a 2.32% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 6099747 0.02447234424342718 0.22924100641919443 chr2 243199373 7597396 0.031239373302167188 0.22741968254792033 chr3 198022430 5928079 0.029936401649045513 0.20224527143159746 chr4 191154276 6373002 0.03333957331930153 0.2102190198758347 chr5 180915260 4999592 0.027634993311233116 0.18789318874618707 chr6 171115067 5384013 0.031464283621500146 0.20573710702102768 chr7 159138663 4618192 0.02901992459242918 0.24097951831860873 chr8 146364022 4434441 0.030297343154453628 0.5553669074172547 chr9 141213431 3527002 0.02497639194107535 0.2075065764924424 chr10 135534747 3587665 0.026470444512653277 0.19212007941468429 chr11 135006516 3577642 0.02649977279615156 0.19665912465062446 chr12 133851895 3525656 0.02633997822742816 0.18334863190489284 chr13 115169878 2811832 0.024414647725857625 0.1813398945755722 chr14 107349540 2673798 0.02490740062789277 0.1894305726406309 chr15 102531392 2145431 0.020924625699024937 0.1666515112151513 chr16 90354753 2457239 0.027195459213971842 0.1932774357140779 chr17 81195210 1826983 0.02250111798466929 0.16758740441042333 chr18 78077248 2108561 0.027006087612104362 0.31316641530660916 chr19 59128983 1296463 0.02192601553793002 0.22752765276246856 chr20 63025520 1635525 0.02595020239420476 0.18479011845967003 chr21 48129895 1243940 0.025845475042071044 0.20312793907213014 chr22 51304566 966221 0.018833041098135397 0.19182441377811643 chrMT 16571 11563 0.6977852875505401 1.0460551665687743 chrX 155270560 2957806 0.01904936776166712 0.16345273622875361 chrY 59373566 738479 0.0124378414461412 0.13528230141502462