BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081884.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,188,660 number of mapped reads = 2,927,864 (91.82%) number of supplementary alignments = 19,331 (0.61%) number of secondary alignments = 0 number of mapped bases = 196,713,792 bp number of sequenced bases = 196,643,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,342 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1168 >>>>>>> ACTG content number of A's = 53,878,370 bp (27.4%) number of C's = 38,551,752 bp (19.6%) number of T's = 59,408,034 bp (30.21%) number of G's = 44,803,063 bp (22.78%) number of N's = 2,136 bp (0%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,605,755 number of insertions = 14,087 mapped reads with insertion percentage = 0.48% number of deletions = 39,433 mapped reads with deletion percentage = 1.33% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.0635X std coverageData = 0.4919X There is a 5.26% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15868722 0.06366572703544036 0.8460446781730416 chr2 243199373 16668534 0.06853855663517686 0.6237623623987544 chr3 198022430 12645033 0.06385656917754216 0.29601749380955455 chr4 191154276 13137769 0.06872861687906998 0.34363689146394943 chr5 180915260 12049441 0.06660267906643143 0.300512578235279 chr6 171115067 11561418 0.06756516654375035 0.3754016737525179 chr7 159138663 10661922 0.06699768490577303 0.6850078824826091 chr8 146364022 10172925 0.06950427339308836 0.5578957355980605 chr9 141213431 8443919 0.059795438296517275 0.47216083946192167 chr10 135534747 9328980 0.06883091020194253 0.5533039488075165 chr11 135006516 8402622 0.06223864039273482 0.4149764326418518 chr12 133851895 8853805 0.06614628055882212 0.30394742373758504 chr13 115169878 5902629 0.05125149997988189 0.26144435661008597 chr14 107349540 5996199 0.05585677404858931 0.3059403189358162 chr15 102531392 5722020 0.05580749357231003 0.2790778163440984 chr16 90354753 5613235 0.06212440202232637 0.3542915165020874 chr17 81195210 5311950 0.06542196269952377 0.33457563957416336 chr18 78077248 5215128 0.06679446488687717 0.8492188842999737 chr19 59128983 3965747 0.06706942684943525 0.648338840396911 chr20 63025520 4130325 0.06553416774665247 0.3119228340445719 chr21 48129895 2670661 0.05548861056106605 0.3167036476683966 chr22 51304566 2341036 0.045630168667638665 0.24775070420859868 chrMT 16571 12390 0.7476917506487236 0.9957083550239214 chrX 155270560 11523149 0.07421335377421193 0.3779125761309405 chrY 59373566 514233 0.00866097549202283 0.21966914995746117