BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008700.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 = 1,947,952 number of mapped reads = 1,315,828 (67.55%) number of supplementary alignments = 7,332 (0.38%) number of secondary alignments = 0 number of mapped bases = 81,186,826 bp number of sequenced bases = 81,141,565 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,009 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.226 >>>>>>> ACTG content number of A's = 24,275,916 bp (29.92%) number of C's = 13,895,408 bp (17.12%) number of T's = 25,158,438 bp (31.01%) number of G's = 17,791,589 bp (21.93%) number of N's = 20,214 bp (0.02%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 900,875 number of insertions = 6,696 mapped reads with insertion percentage = 0.51% number of deletions = 29,531 mapped reads with deletion percentage = 2.22% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.2225X There is a 2.29% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% 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 6838508 0.02743627266629759 0.28731292635689193 chr2 243199373 7127185 0.02930593492936349 0.24182032256943686 chr3 198022430 5827489 0.029428428890605977 0.19681897061441522 chr4 191154276 5200830 0.027207500186917085 0.19048378734950674 chr5 180915260 5141402 0.028418840953493917 0.19106994855277756 chr6 171115067 4855769 0.028377214731184368 0.20428512821927577 chr7 159138663 4405526 0.027683568008862812 0.2716360497388108 chr8 146364022 4225439 0.028869382941663083 0.3409505392929564 chr9 141213431 3363685 0.023819865972947007 0.20749281702143932 chr10 135534747 3915455 0.0288889387162098 0.21682127971736476 chr11 135006516 3609382 0.026734872559780746 0.22354952425531377 chr12 133851895 3723205 0.02781585572621142 0.1915097374550964 chr13 115169878 2860716 0.02483909898732375 0.18112838038690685 chr14 107349540 2469100 0.02300056432472836 0.17991674450836817 chr15 102531392 1979393 0.019305238731178058 0.16081326271411792 chr16 90354753 1943907 0.021514164285303287 0.17739394925673135 chr17 81195210 1810581 0.022299110994355456 0.18066401998572332 chr18 78077248 2242134 0.02871686768468069 0.3034218137815604 chr19 59128983 1137813 0.019242898190892272 0.20521654691768623 chr20 63025520 1569958 0.02490987777649435 0.18296914405569506 chr21 48129895 1165038 0.0242061197100056 0.180740424582118 chr22 51304566 684919 0.013350059330001935 0.13013100299659963 chrMT 16571 36615 2.2095830064570636 2.453672187525648 chrX 155270560 4849056 0.03122971927195986 0.2122503498956764 chrY 59373566 203721 0.0034311733945709107 0.07318588823165223