BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716251.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,626,533 number of mapped reads = 1,531,098 (94.13%) number of supplementary alignments = 29,533 (1.82%) number of secondary alignments = 0 number of mapped bases = 117,849,746 bp number of sequenced bases = 117,806,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,987 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.717 >>>>>>> ACTG content number of A's = 29,653,666 bp (25.17%) number of C's = 24,330,968 bp (20.65%) number of T's = 35,010,319 bp (29.72%) number of G's = 28,807,000 bp (24.45%) number of N's = 4,562 bp (0%) GC percentage = 45.11% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 741,441 number of insertions = 9,487 mapped reads with insertion percentage = 0.61% number of deletions = 21,095 mapped reads with deletion percentage = 1.36% homopolymer indels = 37.54% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3264X There is a 3.19% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 13015963 0.05222038343487216 0.627309784113884 chr2 243199373 11128816 0.04576005218566086 0.3479440317900133 chr3 198022430 7509446 0.037922199015535764 0.2253231385415137 chr4 191154276 5652191 0.029568739545224716 0.2565922015666058 chr5 180915260 7109428 0.03929700568100226 0.23412355301910995 chr6 171115067 7217511 0.04217928395516451 0.25326866649449836 chr7 159138663 7411580 0.046573094559679694 0.4273672810122861 chr8 146364022 7412333 0.050643135510446684 0.36587309939675805 chr9 141213431 3574988 0.025316203810670106 0.2394750997211576 chr10 135534747 6248179 0.04610020041576497 0.39473257805079776 chr11 135006516 3467137 0.025681256747637278 0.25647909438406835 chr12 133851895 4138610 0.030919323181789842 0.20188539584603912 chr13 115169878 2230300 0.0193653066125502 0.1580924538595492 chr14 107349540 2288138 0.02131483749255004 0.18075314898259381 chr15 102531392 2400273 0.023410127895269382 0.1757145319389891 chr16 90354753 3488279 0.03860648039179521 0.23903742484671053 chr17 81195210 2129036 0.026221201964992762 0.2092914419727557 chr18 78077248 3593307 0.046022459705547 0.3610259167557186 chr19 59128983 2897990 0.04901132833622388 0.4652535685552622 chr20 63025520 3162638 0.050180276180188596 0.2709470772864489 chr21 48129895 2045086 0.0424909715676712 0.2730498539495859 chr22 51304566 1828518 0.03564045352220697 0.22439032455520894 chrMT 16571 91539 5.524048035725062 4.146178666406794 chrX 155270560 7423535 0.047810318968386535 0.26707351795844847 chrY 59373566 384925 0.006483103945617819 0.19329457819227167