BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008677.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 = 1,615,515 number of mapped reads = 1,406,341 (87.05%) number of supplementary alignments = 7,721 (0.48%) number of secondary alignments = 0 number of mapped bases = 90,535,160 bp number of sequenced bases = 90,480,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,728 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8435 >>>>>>> ACTG content number of A's = 24,809,767 bp (27.42%) number of C's = 16,426,106 bp (18.15%) number of T's = 28,868,341 bp (31.91%) number of G's = 20,354,908 bp (22.5%) number of N's = 21,348 bp (0.02%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 720,958 number of insertions = 5,849 mapped reads with insertion percentage = 0.41% number of deletions = 31,380 mapped reads with deletion percentage = 2.2% homopolymer indels = 44.77% >>>>>>> Coverage mean coverageData = 0.0292X std coverageData = 0.2751X There is a 2.45% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7542260 0.03025974406699673 0.5054252944745046 chr2 243199373 7918004 0.032557666174575214 0.3000671983555899 chr3 198022430 6591073 0.03328447691506462 0.21243627315043725 chr4 191154276 5513536 0.028843383027434867 0.20135001737740466 chr5 180915260 5004869 0.027664161663311322 0.19192869378917257 chr6 171115067 4943767 0.028891476868018875 0.21644006814580408 chr7 159138663 4975377 0.031264413727040044 0.2940519404638762 chr8 146364022 5816784 0.03974189777321096 0.2988731105140377 chr9 141213431 3360732 0.0237989543643338 0.2328295436012921 chr10 135534747 4679416 0.03452558184212348 0.3120197765543729 chr11 135006516 4080228 0.030222452374076524 0.24336010619870826 chr12 133851895 4015660 0.030000770627864475 0.20126451218995675 chr13 115169878 2719007 0.023608664411366314 0.17706722325211272 chr14 107349540 2963322 0.027604421965850993 0.1965169989074655 chr15 102531392 2414959 0.023553362076660384 0.1765334774406013 chr16 90354753 2468762 0.02732298985975868 0.2139199587996954 chr17 81195210 2326468 0.028652773975213562 0.21250738683934306 chr18 78077248 2117107 0.027115543314231567 0.3538702593486126 chr19 59128983 1607243 0.02718198281881493 0.34282150653891796 chr20 63025520 1921225 0.030483286770184522 0.20255111472579468 chr21 48129895 1057303 0.02196769803881766 0.18006213764275691 chr22 51304566 996728 0.019427666535567226 0.15819854808555697 chrMT 16571 292064 17.625007543298533 9.480156438172424 chrX 155270560 4976160 0.032048316177902623 0.2234497202708734 chrY 59373566 233106 0.003926090610761024 0.12136457788573238