BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231820.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 = 1,185,497 number of mapped reads = 771,396 (65.07%) number of supplementary alignments = 5,353 (0.45%) number of secondary alignments = 0 number of mapped bases = 49,290,325 bp number of sequenced bases = 49,258,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,661 duplication rate = 5.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2436 >>>>>>> ACTG content number of A's = 13,734,559 bp (27.88%) number of C's = 8,115,426 bp (16.48%) number of T's = 16,585,034 bp (33.67%) number of G's = 10,817,724 bp (21.96%) number of N's = 5,768 bp (0.01%) GC percentage = 38.44% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 494,283 number of insertions = 4,292 mapped reads with insertion percentage = 0.55% number of deletions = 17,987 mapped reads with deletion percentage = 2.3% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.2375X There is a 1.33% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 4291070 0.01721588489041317 0.31705648003999415 chr2 243199373 3362938 0.013827905715858898 0.2154746966557187 chr3 198022430 4584456 0.023151195548908272 0.1814413160723485 chr4 191154276 2051506 0.010732200413868848 0.12458123495567608 chr5 180915260 2822287 0.015600049437510135 0.14773521581884425 chr6 171115067 3655479 0.021362695080498085 0.19173246981932898 chr7 159138663 2932671 0.018428400394440915 0.1951966287978177 chr8 146364022 2617632 0.01788439511453163 0.7136614334204335 chr9 141213431 2018392 0.014293201331536233 0.1543210510418841 chr10 135534747 2283651 0.016849192185381067 0.16922548936900472 chr11 135006516 2641719 0.01956734443839733 0.1788851490624301 chr12 133851895 1492020 0.011146797734914398 0.12697244426173088 chr13 115169878 1944219 0.016881315095254333 0.15314700529361433 chr14 107349540 2324490 0.021653469591020137 0.17608013592466407 chr15 102531392 998600 0.00973945618528226 0.11773095372923553 chr16 90354753 1336710 0.0147940197457017 0.1466822456863936 chr17 81195210 1109538 0.013665067188076734 0.14030315781889774 chr18 78077248 944879 0.01210184815940234 0.20667733778919323 chr19 59128983 1345111 0.022748759267515222 0.22457385829301105 chr20 63025520 1149282 0.01823518473151828 0.16348134441923856 chr21 48129895 851336 0.01768829954854462 0.15733276014855851 chr22 51304566 379390 0.007394858383559857 0.09828989487742712 chrMT 16571 44050 2.658258403234566 3.6851703996679195 chrX 155270560 1976003 0.012726192267226962 0.13578117271982323 chrY 59373566 132896 0.0022383024795916756 0.06266284247517148