BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751186.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,001,127 number of mapped reads = 4,381,128 (87.6%) number of supplementary alignments = 157,554 (3.15%) number of secondary alignments = 0 number of mapped bases = 429,835,969 bp number of sequenced bases = 429,707,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,929 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1994 >>>>>>> ACTG content number of A's = 125,866,175 bp (29.29%) number of C's = 88,923,844 bp (20.69%) number of T's = 126,621,996 bp (29.47%) number of G's = 88,292,845 bp (20.55%) number of N's = 2,378 bp (0%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,638,929 number of insertions = 108,736 mapped reads with insertion percentage = 2.43% number of deletions = 58,867 mapped reads with deletion percentage = 1.32% homopolymer indels = 48.91% >>>>>>> Coverage mean coverageData = 0.1388X std coverageData = 1.4229X There is a 10.88% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 51917951 0.20829617511765397 4.041224839616168 chr2 243199373 32175709 0.13230177612341132 0.5917202295657515 chr3 198022430 28246225 0.14264154318275965 0.5148107702677649 chr4 191154276 20070004 0.1049937486096309 0.4820322934695239 chr5 180915260 34966342 0.19327469667290642 0.5284400162397094 chr6 171115067 24643911 0.14401952693037837 0.9488779256634047 chr7 159138663 24038980 0.15105681766347376 0.7921854720739 chr8 146364022 20972291 0.14328856718627206 0.5253181382763731 chr9 141213431 18567932 0.1314884276128097 0.7234027252661486 chr10 135534747 21583387 0.1592461525751769 2.030081515728403 chr11 135006516 19424916 0.14388132199485837 0.6933939652648529 chr12 133851895 22683185 0.16946480287036653 0.48860709218160775 chr13 115169878 12434726 0.10796856101558083 0.3815585657800011 chr14 107349540 9318234 0.08680273804619935 0.37581640651368203 chr15 102531392 10231676 0.09979066703785705 0.36750703189065564 chr16 90354753 12091230 0.13381952358388938 0.9987298002687243 chr17 81195210 11508627 0.14174022088248803 0.6905626278657401 chr18 78077248 8965278 0.11482574283355888 1.384268805890391 chr19 59128983 7834044 0.13249076176398975 2.7674868890589783 chr20 63025520 7622575 0.12094426194341594 0.4260684861362064 chr21 48129895 5563632 0.11559617987946992 0.45194054515171495 chr22 51304566 4601564 0.0896911202796258 0.3544535892141401 chrMT 16571 978213 59.031621507452776 25.966211098043537 chrX 155270560 18310109 0.11792389362155968 0.4714497571827711 chrY 59373566 1085228 0.018277965652256763 0.7014447173830933