BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716217.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 = 1,182,994 number of mapped reads = 1,085,003 (91.72%) number of supplementary alignments = 6,225 (0.53%) number of secondary alignments = 0 number of mapped bases = 64,043,507 bp number of sequenced bases = 64,023,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,839 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6356 >>>>>>> ACTG content number of A's = 16,865,736 bp (26.34%) number of C's = 12,481,306 bp (19.49%) number of T's = 20,021,390 bp (31.27%) number of G's = 14,654,503 bp (22.89%) number of N's = 895 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 315,843 number of insertions = 4,288 mapped reads with insertion percentage = 0.39% number of deletions = 12,342 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.19% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2225X There is a 1.91% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4870496 0.019540557132654044 0.3047830119529768 chr2 243199373 6519355 0.026806627498994415 0.2364602832865681 chr3 198022430 4914189 0.024816325100141434 0.17425868692742247 chr4 191154276 3133662 0.01639336595326803 0.14585568320526185 chr5 180915260 3346840 0.018499489761117996 0.14411887795392425 chr6 171115067 3738685 0.0218489526699598 0.16610553434392566 chr7 159138663 4165842 0.026177434958090606 0.4889699348653555 chr8 146364022 5340370 0.03648690386494025 0.2452161958761707 chr9 141213431 2567857 0.018184226399824532 0.1598832329796979 chr10 135534747 3089639 0.02279591815669232 0.303985240176993 chr11 135006516 2273409 0.016839253892012147 0.16501367769715342 chr12 133851895 3150840 0.023539748914275738 0.17987016683487897 chr13 115169878 1656917 0.014386721847530306 0.12595420311605582 chr14 107349540 1666661 0.015525553253418692 0.1341249755627024 chr15 102531392 1570977 0.01532191233685777 0.13435983259764867 chr16 90354753 1996121 0.022092042020191233 0.1645476165512881 chr17 81195210 2061657 0.02539136237223846 0.1717836675766713 chr18 78077248 1201568 0.01538947684221657 0.23536841992779997 chr19 59128983 1289313 0.021805093451378998 0.293524386002048 chr20 63025520 1485289 0.02356646958248024 0.16873130565714742 chr21 48129895 675202 0.01402874450484465 0.12812506258151085 chr22 51304566 869775 0.016953169431352368 0.1376069948123108 chrMT 16571 21278 1.2840504495805927 1.3263767619773625 chrX 155270560 2297700 0.014798040272412234 0.14169987053127392 chrY 59373566 139865 0.002355677945973466 0.06769686096683057