BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549064.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 = 11,152,142 number of mapped reads = 9,683,492 (86.83%) number of secondary alignments = 0 number of mapped bases = 384,055,544 bp number of sequenced bases = 384,017,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 458,587 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3892 >>>>>>> ACTG content number of A's = 113,997,569 bp (29.69%) number of C's = 78,296,521 bp (20.39%) number of T's = 114,018,985 bp (29.69%) number of G's = 77,696,838 bp (20.23%) number of N's = 7,318 bp (0%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 1,335,563 number of insertions = 11,053 mapped reads with insertion percentage = 0.11% number of deletions = 30,630 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.1241X std coverageData = 1.6924X There is a 10.4% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 31422905 0.12606951538949224 4.635993938766446 chr2 243199373 33540810 0.13791487036440675 1.0771708953327883 chr3 198022430 26756868 0.13512039014974211 0.4460063690282314 chr4 191154276 26785704 0.1401261042154244 0.48676966095446683 chr5 180915260 24590718 0.13592395688456574 0.4708955582365657 chr6 171115067 23326392 0.1363199185726877 0.6306812798816943 chr7 159138663 22049020 0.1385522511270564 1.6233712899016501 chr8 146364022 20498918 0.14005435024189208 2.063075580590337 chr9 141213431 16311928 0.11551258180250575 0.9787868723760941 chr10 135534747 18575723 0.1370550608693725 1.3235827115836638 chr11 135006516 17671738 0.13089544507614728 0.9155904853023514 chr12 133851895 17611016 0.13157091276145175 0.5302167640537517 chr13 115169878 12875667 0.11179717495229091 0.36500523590733 chr14 107349540 11804468 0.10996291181126626 0.5117762134096071 chr15 102531392 10560719 0.10299985978928287 0.3646099512158202 chr16 90354753 9974311 0.11039055134155477 0.611639187406284 chr17 81195210 9069781 0.11170339974488643 0.48522279390284667 chr18 78077248 10728163 0.13740447153055393 2.3509143118455076 chr19 59128983 7100151 0.12007903129333376 3.6881938035234896 chr20 63025520 7345408 0.11654656716834705 0.45865591812643725 chr21 48129895 4962135 0.10309881207927006 0.5372907230128285 chr22 51304566 3635219 0.07085566224261598 0.3521794696496944 chrMT 16571 10309 0.6221109166616378 0.9885488389351642 chrX 155270560 13424948 0.0864616447573835 0.6706226783498618 chrY 59373566 3422525 0.05764391850743814 0.5535647596512128