BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004103.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 = 3,638,221 number of mapped reads = 2,442,667 (67.14%) number of supplementary alignments = 26,836 (0.74%) number of secondary alignments = 0 number of mapped bases = 165,605,562 bp number of sequenced bases = 165,529,259 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 296,480 duplication rate = 9.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4223 >>>>>>> ACTG content number of A's = 46,644,310 bp (28.18%) number of C's = 31,030,088 bp (18.75%) number of T's = 52,740,915 bp (31.86%) number of G's = 35,091,527 bp (21.2%) number of N's = 22,419 bp (0.01%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,579,580 number of insertions = 13,707 mapped reads with insertion percentage = 0.56% number of deletions = 45,966 mapped reads with deletion percentage = 1.86% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.5586X There is a 2.35% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 12185393 0.0488881149066425 0.8846039407171671 chr2 243199373 12465827 0.051257644484141 0.5561304465329309 chr3 198022430 12739860 0.06433543917221902 0.5040504462611932 chr4 191154276 8718351 0.04560897711751946 0.42150054703894807 chr5 180915260 10165563 0.056189638176458966 0.4628224983247333 chr6 171115067 8693921 0.050807454611813935 0.49330997043299607 chr7 159138663 8137417 0.05113412948555437 0.5974278055201417 chr8 146364022 14934454 0.10203637339236278 0.7720855488900414 chr9 141213431 6025207 0.04266737913902821 0.4588704648610957 chr10 135534747 5917214 0.04365828048507738 0.5383210764380054 chr11 135006516 6001687 0.04445479505596604 0.45567585564481994 chr12 133851895 6832657 0.05104639721387583 0.4374675353650274 chr13 115169878 4122868 0.035798145067063455 0.3633132169839751 chr14 107349540 5979537 0.05570156145988143 0.4754676365269297 chr15 102531392 6918319 0.06747512995824732 0.5177799153717222 chr16 90354753 3449507 0.038177371809095646 0.3944304610819014 chr17 81195210 4422353 0.05446568830846056 0.4788301928581225 chr18 78077248 3892533 0.04985489498810204 0.7485668338262336 chr19 59128983 2087315 0.03530104686562933 0.6549074381959656 chr20 63025520 2799364 0.04441635705663357 0.4099144774821895 chr21 48129895 2031802 0.04221496847229773 0.4023669015119483 chr22 51304566 1224448 0.023866257829761196 0.28108699984071295 chrMT 16571 177970 10.739846720173798 8.381645952305357 chrX 155270560 15096149 0.09722479908618865 0.6555896456619272 chrY 59373566 585846 0.009867118306486762 0.20554992063195582