BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548968.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 = 7,031,825 number of mapped reads = 6,022,286 (85.64%) number of secondary alignments = 0 number of mapped bases = 237,917,950 bp number of sequenced bases = 237,895,982 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 284,407 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.5663 >>>>>>> ACTG content number of A's = 66,972,022 bp (28.15%) number of C's = 51,378,824 bp (21.6%) number of T's = 68,045,564 bp (28.6%) number of G's = 51,499,254 bp (21.65%) number of N's = 318 bp (0%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 769,051 number of insertions = 8,286 mapped reads with insertion percentage = 0.14% number of deletions = 17,218 mapped reads with deletion percentage = 0.29% homopolymer indels = 37.92% >>>>>>> Coverage mean coverageData = 0.0769X std coverageData = 0.8612X There is a 6.43% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.14% 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% 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 19180567 0.07695293565587545 1.6031119174958002 chr2 243199373 20296552 0.0834564322663776 0.8711115902277871 chr3 198022430 15960529 0.08059960177238508 0.33234252350313254 chr4 191154276 15831453 0.08282029223348371 0.38376052127133686 chr5 180915260 14800473 0.08180887007541542 0.35521292354789796 chr6 171115067 13849772 0.08093835477386688 0.366635302451423 chr7 159138663 13874452 0.0871846711443089 1.3791957334271585 chr8 146364022 12291127 0.08397642283976044 1.3893243717141628 chr9 141213431 10189341 0.07215560820131904 0.9017927332990063 chr10 135534747 11442349 0.08442373083855759 0.7135739901568995 chr11 135006516 11031756 0.08171276710821869 0.5944170972741035 chr12 133851895 10927527 0.08163894130897437 0.3777700506055459 chr13 115169878 7545329 0.0655147780915423 0.28750264341060416 chr14 107349540 7345854 0.0684293011409271 0.507146586024832 chr15 102531392 6606856 0.06443739689011536 0.3019408724627501 chr16 90354753 6702599 0.07418092327694151 0.45272484423340686 chr17 81195210 6447739 0.07941033713688282 0.3715039817719645 chr18 78077248 6312958 0.08085528321899871 1.7302980935085046 chr19 59128983 5425402 0.0917553748556778 1.639185783481658 chr20 63025520 4781911 0.07587261477572894 0.35956778700157926 chr21 48129895 3010977 0.06255939266021669 0.4694577824086145 chr22 51304566 2670446 0.052050844753272055 0.39656227732652105 chrMT 16571 6534 0.3943033009474383 0.7135685161587488 chrX 155270560 9109930 0.05867132829301318 0.4708591134409919 chrY 59373566 2275517 0.038325422461571536 0.3796760836111727