BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505960.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 7,280,496 number of mapped reads = 5,427,382 (74.55%) number of supplementary alignments = 290 (0%) number of secondary alignments = 0 number of mapped bases = 253,219,657 bp number of sequenced bases = 253,170,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,724 duplication rate = 5.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2066 >>>>>>> ACTG content number of A's = 74,140,655 bp (29.28%) number of C's = 52,609,506 bp (20.78%) number of T's = 73,439,579 bp (29.01%) number of G's = 52,979,481 bp (20.93%) number of N's = 1,141 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,282,189 number of insertions = 11,607 mapped reads with insertion percentage = 0.21% number of deletions = 35,825 mapped reads with deletion percentage = 0.66% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0818X std coverageData = 0.6329X There is a 6.34% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% 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% 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 20540049 0.08240721293930096 1.0587793122477551 chr2 243199373 21405745 0.08801727050505184 0.5470425582875322 chr3 198022430 17195305 0.08683513781746846 0.36745563342302273 chr4 191154276 16786548 0.08781675383500184 0.3767710453045343 chr5 180915260 16190153 0.08949025637748856 0.3742000088320214 chr6 171115067 14717571 0.08600979012561179 0.4216602217726668 chr7 159138663 14119267 0.08872304651698626 0.9556630333448923 chr8 146364022 13301226 0.09087770217191764 0.8681789105791599 chr9 141213431 10740827 0.0760609449394371 0.4819316929030651 chr10 135534747 12123521 0.08944954167361968 0.6561492839990548 chr11 135006516 11711175 0.08674525754001385 0.5769299528640435 chr12 133851895 11047772 0.08253728495961898 0.3802016381995683 chr13 115169878 6870950 0.059659262641573695 0.3012296328500999 chr14 107349540 7777968 0.0724546001780725 1.1748175973002113 chr15 102531392 7149748 0.06973228257741786 0.3251797265806839 chr16 90354753 7090505 0.07847406765640763 0.4064326942283423 chr17 81195210 6510416 0.08018226690958741 0.41456293254347526 chr18 78077248 6823416 0.08739314172548704 0.9980115617007118 chr19 59128983 4750013 0.08033307456006811 0.8104207963836729 chr20 63025520 5219593 0.08281713502720803 0.3764868205059836 chr21 48129895 3256211 0.06765464582875155 0.3590279057037029 chr22 51304566 2686441 0.05236261037662807 0.28458625478109045 chrMT 16571 52758 3.1837547522780762 2.580207372933662 chrX 155270560 14396252 0.09271720279749104 0.438238451363114 chrY 59373566 756227 0.01273676234976353 0.19708071213268152