BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548924.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,002,677 number of mapped reads = 6,108,896 (87.24%) number of secondary alignments = 0 number of mapped bases = 241,962,114 bp number of sequenced bases = 241,934,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 183,648 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3271 >>>>>>> ACTG content number of A's = 72,066,748 bp (29.79%) number of C's = 48,887,440 bp (20.21%) number of T's = 72,108,394 bp (29.8%) number of G's = 48,869,746 bp (20.2%) number of N's = 2,226 bp (0%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 664,695 number of insertions = 7,554 mapped reads with insertion percentage = 0.12% number of deletions = 20,605 mapped reads with deletion percentage = 0.34% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.0782X std coverageData = 0.8705X There is a 6.52% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 18588159 0.07457617929064257 0.7981495269103479 chr2 243199373 20383018 0.08381196772246613 0.4482431793725829 chr3 198022430 16671770 0.08419132115488129 0.3359081379203492 chr4 191154276 16283299 0.08518406880942596 0.3455748148884985 chr5 180915260 15339601 0.084788872978432 0.3412203775220597 chr6 171115067 14243755 0.08324079959598181 0.364175803233961 chr7 159138663 13458987 0.0845739605088928 0.6485406003216118 chr8 146364022 12829257 0.08765307774884733 3.4183093882000612 chr9 141213431 10207308 0.07228284114136424 0.43736799567084267 chr10 135534747 11022821 0.08132837699545785 0.410698068465211 chr11 135006516 10875768 0.08055735620938474 0.4770419087483845 chr12 133851895 10948289 0.08179405304646602 0.33976709525434845 chr13 115169878 8155751 0.0708149660452015 0.3044985487889604 chr14 107349540 7536246 0.07020287185208246 0.3523128422045091 chr15 102531392 6892007 0.06721850611371784 0.29814925141670306 chr16 90354753 6402022 0.07085429141729821 0.33154006855150425 chr17 81195210 5928344 0.0730134696369404 0.3285082091275235 chr18 78077248 6504725 0.08331140206171202 0.7871029687293425 chr19 59128983 4355214 0.0736561628330391 0.7339968390084496 chr20 63025520 4717823 0.07485575684262502 0.3231896712950835 chr21 48129895 3089326 0.06418725825186197 0.3218232184804022 chr22 51304566 2507220 0.04886933455396543 0.2768008737274303 chrMT 16571 7447 0.44939955343672683 0.7844946592997935 chrX 155270560 14280911 0.09197436397472901 0.4133029895356514 chrY 59373566 733046 0.012346336078247347 0.16959223734485607