BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004160.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,898,131 number of mapped reads = 2,881,178 (73.91%) number of supplementary alignments = 21,061 (0.54%) number of secondary alignments = 0 number of mapped bases = 185,144,463 bp number of sequenced bases = 185,053,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,491 duplication rate = 5.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0869 >>>>>>> ACTG content number of A's = 50,906,769 bp (27.51%) number of C's = 34,790,270 bp (18.8%) number of T's = 58,407,666 bp (31.56%) number of G's = 40,926,215 bp (22.12%) number of N's = 22,977 bp (0.01%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,931,750 number of insertions = 16,669 mapped reads with insertion percentage = 0.57% number of deletions = 54,692 mapped reads with deletion percentage = 1.88% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.5751X There is a 4.27% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.32% 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% 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 15274376 0.06128119536360152 1.0819148078354754 chr2 243199373 16299630 0.06702167772447341 0.6895663540252693 chr3 198022430 11377488 0.05745555187864324 0.3210026908395456 chr4 191154276 12803239 0.0669785644763709 0.41524118914712826 chr5 180915260 10641199 0.05881869224298713 0.3237820186974711 chr6 171115067 11157977 0.06520744897350272 0.4380575133780155 chr7 159138663 9811684 0.061654935482271835 0.7497951443685984 chr8 146364022 9991179 0.06826253380765937 0.6793707208596302 chr9 141213431 8033829 0.05689139441700839 0.5182115321399071 chr10 135534747 8118452 0.05989941457595372 0.6286767067075791 chr11 135006516 7798670 0.05776513779527501 0.4756344966601471 chr12 133851895 8156611 0.06093758328935126 0.3367272723114978 chr13 115169878 5885918 0.0511064012762087 0.2986780672861473 chr14 107349540 5600905 0.05217446670009019 0.3509984078354855 chr15 102531392 5126375 0.04999810204468891 0.2975791954973458 chr16 90354753 5111628 0.056572873371697446 0.37543725715098625 chr17 81195210 4544426 0.05596913906620846 0.34966376320266057 chr18 78077248 5539097 0.0709438042693308 1.0069611385800903 chr19 59128983 3303086 0.05586238478006632 0.7198886799753212 chr20 63025520 3729782 0.059178916730873464 0.34100724685903305 chr21 48129895 2554821 0.05308179043399118 0.3720360246844399 chr22 51304566 1945260 0.037915923506691394 0.25465748345126427 chrMT 16571 110389 6.6615774545893425 5.255146435975247 chrX 155270560 11269845 0.07258198205764184 0.4143730412711813 chrY 59373566 958597 0.01614518151057324 0.3370491885496659