BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926896.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 29,069,352 number of mapped reads = 27,902,346 (95.99%) number of supplementary alignments = 877,519 (3.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,030,551 number of mapped paired reads (second in pair) = 13,871,795 number of mapped paired reads (both in pair) = 27,420,688 number of mapped paired reads (singletons) = 481,658 number of mapped bases = 2,464,116,086 bp number of sequenced bases = 2,462,077,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,461,804 duplication rate = 9.7% >>>>>>> Insert size mean insert size = 363,344.9627 std insert size = 5,939,426.6704 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.4707 >>>>>>> ACTG content number of A's = 692,558,605 bp (28.13%) number of C's = 478,464,281 bp (19.43%) number of T's = 707,357,653 bp (28.73%) number of G's = 583,509,907 bp (23.7%) number of N's = 187,368 bp (0.01%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 26,265,348 number of insertions = 434,476 mapped reads with insertion percentage = 1.53% number of deletions = 1,379,300 mapped reads with deletion percentage = 4.81% homopolymer indels = 51.67% >>>>>>> Coverage mean coverageData = 0.796X std coverageData = 2.6606X There is a 30.77% of reference with a coverageData >= 1X There is a 16.72% of reference with a coverageData >= 2X There is a 9.67% of reference with a coverageData >= 3X There is a 6.12% of reference with a coverageData >= 4X There is a 4.05% of reference with a coverageData >= 5X There is a 2.79% of reference with a coverageData >= 6X There is a 1.98% of reference with a coverageData >= 7X There is a 1.44% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 0.81% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 201619056 0.8089009174424484 2.3344171779522567 chr2 243199373 204730502 0.8418216686767527 3.103286037628872 chr3 198022430 153978483 0.7775810194834999 1.8418179138990145 chr4 191154276 131346525 0.6871231329400134 1.834257059826276 chr5 180915260 133400289 0.7373633876987491 1.7437703648107554 chr6 171115067 135383406 0.7911834321404322 1.8456981042480367 chr7 159138663 117606921 0.7390216731932705 1.9627317756016547 chr8 146364022 116152048 0.7935833301984555 1.9528778335242234 chr9 141213431 104291646 0.7385391407988664 2.639680439489713 chr10 135534747 120684739 0.8904339416371213 6.284741234727926 chr11 135006516 118853738 0.880355567430538 2.2982124686559895 chr12 133851895 109665989 0.8193084528239215 2.0449214634347093 chr13 115169878 67798876 0.5886858367601987 1.5736410371424494 chr14 107349540 73696212 0.6865070125125827 1.76362484969212 chr15 102531392 79371929 0.7741231973130727 1.9866510857801298 chr16 90354753 156713622 1.7344258801747818 5.87498083410448 chr17 81195210 72320658 0.8907010401229334 2.1003362017151987 chr18 78077248 61710961 0.7903834033699548 2.298042580110141 chr19 59128983 49694324 0.8404393493458191 2.1979922476708165 chr20 63025520 58466003 0.9276560193394676 2.162545386317623 chr21 48129895 29587572 0.6147441626456904 2.146006039168046 chr22 51304566 38090126 0.7424315021006123 2.0393751577535166 chrMT 16571 1832962 110.61263653370345 77.32645158407021 chrX 155270560 123422989 0.7948898297268974 1.8582240465040485 chrY 59373566 3696510 0.06225851416773586 1.2514364745117725