BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617729.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 43,414,462 number of mapped reads = 42,782,181 (98.54%) number of supplementary alignments = 1,034,428 (2.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,542,926 number of mapped paired reads (second in pair) = 21,239,255 number of mapped paired reads (both in pair) = 42,400,204 number of mapped paired reads (singletons) = 381,977 number of mapped bases = 5,698,567,312 bp number of sequenced bases = 5,694,341,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,281,758 duplication rate = 27.05% >>>>>>> Insert size mean insert size = 234,707.622 std insert size = 5,191,189.2098 median insert size = 279 >>>>>>> Mapping quality mean mapping quality = 53.3222 >>>>>>> ACTG content number of A's = 1,624,980,891 bp (28.54%) number of C's = 1,097,866,663 bp (19.28%) number of T's = 1,685,763,015 bp (29.6%) number of G's = 1,285,506,815 bp (22.58%) number of N's = 223,802 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 62,671,840 number of insertions = 960,121 mapped reads with insertion percentage = 2.14% number of deletions = 2,231,572 mapped reads with deletion percentage = 5.02% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 1.8408X std coverageData = 34.3665X There is a 34.35% of reference with a coverageData >= 1X There is a 23.4% of reference with a coverageData >= 2X There is a 16.4% of reference with a coverageData >= 3X There is a 12.05% of reference with a coverageData >= 4X There is a 8.97% of reference with a coverageData >= 5X There is a 6.84% of reference with a coverageData >= 6X There is a 5.27% of reference with a coverageData >= 7X There is a 4.12% of reference with a coverageData >= 8X There is a 3.26% of reference with a coverageData >= 9X There is a 2.61% of reference with a coverageData >= 10X There is a 2.1% of reference with a coverageData >= 11X There is a 1.71% of reference with a coverageData >= 12X There is a 1.4% of reference with a coverageData >= 13X There is a 1.16% of reference with a coverageData >= 14X There is a 0.97% of reference with a coverageData >= 15X There is a 0.81% of reference with a coverageData >= 16X There is a 0.69% of reference with a coverageData >= 17X There is a 0.59% of reference with a coverageData >= 18X There is a 0.51% of reference with a coverageData >= 19X There is a 0.44% of reference with a coverageData >= 20X There is a 0.39% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2009843487 8.063544551810766 108.13143747026074 chr2 243199373 358767342 1.4751984660749926 14.029499033966285 chr3 198022430 346644281 1.7505303868859705 3.7209544135083874 chr4 191154276 242648703 1.2693867386989555 10.370400618916772 chr5 180915260 209817630 1.1597563964477071 3.0759237124578123 chr6 171115067 234678789 1.3714677095033367 6.895523240889723 chr7 159138663 242562141 1.5242187940211613 14.697456222931903 chr8 146364022 181965653 1.243240316257502 3.601768211083865 chr9 141213431 147450533 1.044167909212545 24.215047861843882 chr10 135534747 226884231 1.6739930978732709 55.554539217041885 chr11 135006516 164239451 1.216529808087189 8.835088398571106 chr12 133851895 188425069 1.4077131220293893 8.500065868887383 chr13 115169878 104191487 0.904676542246576 2.395864797355134 chr14 107349540 154688662 1.4409811350845099 3.5037320323030956 chr15 102531392 104441036 1.018624969024121 4.268112906151214 chr16 90354753 79695716 0.8820312529657405 6.7860690943496484 chr17 81195210 79836489 0.9832659956172292 12.20056225320581 chr18 78077248 113357111 1.4518584338423404 20.945268119821677 chr19 59128983 74170082 1.2543777727413306 8.929906201093372 chr20 63025520 79300071 1.2582216061049556 4.1314603437082695 chr21 48129895 43994544 0.914079367927148 5.753428626416367 chr22 51304566 34033724 0.6633663756165484 2.3420247550480062 chrMT 16571 1580921 95.40287248808158 55.33366385353838 chrX 155270560 223000428 1.4362054725635047 4.469600646919009 chrY 59373566 52349731 0.881700974470693 21.42709652294067