BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716323.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,208,887 number of mapped reads = 2,024,009 (91.63%) number of supplementary alignments = 8,421 (0.38%) number of secondary alignments = 0 number of mapped bases = 117,991,600 bp number of sequenced bases = 117,959,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,033 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9557 >>>>>>> ACTG content number of A's = 29,582,227 bp (25.08%) number of C's = 21,075,316 bp (17.87%) number of T's = 36,988,467 bp (31.36%) number of G's = 30,310,243 bp (25.7%) number of N's = 3,393 bp (0%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 579,239 number of insertions = 7,807 mapped reads with insertion percentage = 0.38% number of deletions = 20,262 mapped reads with deletion percentage = 0.99% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3859X There is a 3.34% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 12309842 0.049387407544312596 0.9038939108202163 chr2 243199373 11407006 0.04690392848998011 0.4503214968695539 chr3 198022430 8269321 0.04175951683857228 0.23235791270568942 chr4 191154276 5578148 0.02918139273013176 0.20248597349452527 chr5 180915260 5276801 0.029167252115714287 0.19530946177427927 chr6 171115067 8199468 0.047917861026229795 0.2897587531281706 chr7 159138663 6808750 0.04278501447508077 0.43355651537740336 chr8 146364022 6987000 0.04773714130375564 0.29903091095596945 chr9 141213431 4933036 0.034933192721590345 0.29767146959481616 chr10 135534747 6457545 0.047644940820968956 0.36984287056703624 chr11 135006516 3952838 0.029278868288105442 0.26356202508723 chr12 133851895 4799076 0.03585362762327721 0.22168709321036226 chr13 115169878 2697276 0.023419977921657606 0.17072919240252557 chr14 107349540 2613117 0.024342135047807377 0.1991764602193639 chr15 102531392 2493248 0.024316923347729443 0.17600297443455168 chr16 90354753 2498784 0.027655257936458528 0.20838155023909888 chr17 81195210 2596963 0.03198418970774261 0.20864108520044883 chr18 78077248 4223380 0.05409232661479052 0.5160376778217579 chr19 59128983 2923674 0.04944570076573108 0.5100045603129051 chr20 63025520 1813393 0.028772360783377908 0.19177772880101976 chr21 48129895 1510612 0.03138614784013138 0.21589306597932562 chr22 51304566 1420031 0.027678452635190403 0.1851348455565474 chrMT 16571 173051 10.443002836280249 6.2322397094372155 chrX 155270560 7772666 0.05005885210950485 0.300882255928806 chrY 59373566 276574 0.004658200923959999 0.1074898229173111