BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174017.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,125,814 number of mapped reads = 3,041,051 (97.29%) number of supplementary alignments = 312,390 (9.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,522,848 number of mapped paired reads (second in pair) = 1,518,203 number of mapped paired reads (both in pair) = 2,983,618 number of mapped paired reads (singletons) = 57,433 number of mapped bases = 358,320,433 bp number of sequenced bases = 358,106,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,336,942 duplication rate = 63.83% >>>>>>> Insert size mean insert size = 986,177.2979 std insert size = 9,250,216.2963 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.4932 >>>>>>> ACTG content number of A's = 107,950,318 bp (30.14%) number of C's = 69,806,635 bp (19.49%) number of T's = 107,876,101 bp (30.12%) number of G's = 72,468,969 bp (20.24%) number of N's = 4,172 bp (0%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 3,725,129 number of insertions = 38,806 mapped reads with insertion percentage = 1.23% number of deletions = 87,170 mapped reads with deletion percentage = 2.79% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.1157X std coverageData = 1.8527X There is a 2.53% of reference with a coverageData >= 1X There is a 1.97% of reference with a coverageData >= 2X There is a 1.49% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 0.91% of reference with a coverageData >= 5X There is a 0.73% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 30659492 0.12300668249889736 1.5874184256717867 chr2 243199373 32564143 0.13389895951746553 5.068618872193523 chr3 198022430 27977705 0.14128553517901987 1.0723472331454365 chr4 191154276 22373013 0.11704165592403488 1.1503970624196098 chr5 180915260 25035224 0.13838094144186622 1.0604984700570903 chr6 171115067 21746414 0.12708649437632513 1.045461997045839 chr7 159138663 27976822 0.17580153981813962 1.9869774722503595 chr8 146364022 14627312 0.09993789320711616 1.0439600760675278 chr9 141213431 14353374 0.10164312203419235 1.0444252866762798 chr10 135534747 14393489 0.10619777819779307 1.9223813448816847 chr11 135006516 18162732 0.13453226213170333 1.0629392296171178 chr12 133851895 12570950 0.09391686236492953 0.8715945540525328 chr13 115169878 12149231 0.1054896576342644 0.9339613920479601 chr14 107349540 8249482 0.0768469245420148 0.7881544096884824 chr15 102531392 7795786 0.07603316260448312 0.7697332846272459 chr16 90354753 13870110 0.15350725379106508 1.508083714870341 chr17 81195210 8488080 0.10453917170729653 0.9651654518813956 chr18 78077248 5819842 0.07453953807388293 1.2524459851216103 chr19 59128983 6835540 0.11560388244796972 1.6320217149292355 chr20 63025520 10376062 0.16463270751276626 1.1457963702579732 chr21 48129895 5641677 0.11721772923045022 1.005812111257893 chr22 51304566 3185038 0.06208098515052247 0.6692147054309353 chrMT 16571 1131248 68.26673103614749 56.55063420598165 chrX 155270560 11788390 0.07592160419850356 0.7780647130777166 chrY 59373566 549277 0.009251204483827028 0.44633748813094776