BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617668.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,194,521 (94.36%) number of supplementary alignments = 162,669 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,246,186 number of mapped paired reads (second in pair) = 14,948,335 number of mapped paired reads (both in pair) = 29,506,452 number of mapped paired reads (singletons) = 688,069 number of mapped bases = 2,923,998,775 bp number of sequenced bases = 2,922,220,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,949,362 duplication rate = 10.75% >>>>>>> Insert size mean insert size = 41,868.3753 std insert size = 1,910,416.4301 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.59 >>>>>>> ACTG content number of A's = 870,166,852 bp (29.78%) number of C's = 582,001,961 bp (19.92%) number of T's = 869,147,065 bp (29.74%) number of G's = 597,596,957 bp (20.45%) number of N's = 3,307,903 bp (0.11%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 42,222,607 number of insertions = 457,375 mapped reads with insertion percentage = 1.49% number of deletions = 1,074,258 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.9445X std coverageData = 10.5871X There is a 33.26% of reference with a coverageData >= 1X There is a 19.23% of reference with a coverageData >= 2X There is a 11.73% of reference with a coverageData >= 3X There is a 7.48% of reference with a coverageData >= 4X There is a 4.92% of reference with a coverageData >= 5X There is a 3.33% of reference with a coverageData >= 6X There is a 2.3% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% 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 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179518616 0.7202333750654928 10.26749952322945 chr2 243199373 302220473 1.242686069753971 12.111741943705054 chr3 198022430 244601718 1.235222282647476 2.478372902310073 chr4 191154276 163698412 0.8563680364649546 8.325067447080214 chr5 180915260 193273407 1.068309035954181 2.324648622218779 chr6 171115067 141726052 0.8282499868933225 5.737096629565003 chr7 159138663 228525410 1.4360143895390147 13.320122938724722 chr8 146364022 129909390 0.8875773446564621 4.103036957609593 chr9 141213431 120142772 0.8507885627394748 20.514770002944324 chr10 135534747 123742055 0.9129913748243467 21.607404239779406 chr11 135006516 160797566 1.1910355941634698 11.853768984064898 chr12 133851895 124823098 0.9325463640242075 2.193624672564251 chr13 115169878 125739764 1.0917764799577194 2.299205682732052 chr14 107349540 83791571 0.7805489525153065 2.472442450971105 chr15 102531392 62607998 0.6106227251844977 1.6557277219606064 chr16 90354753 81073240 0.8972769811013706 16.76258880828324 chr17 81195210 71918024 0.8857422008022394 12.52344849305048 chr18 78077248 54033483 0.6920515820434655 18.160093560172214 chr19 59128983 30995388 0.5241995790795184 6.0852046554333645 chr20 63025520 79161451 1.2560221795869355 3.0240620346054756 chr21 48129895 42725640 0.8877152131746807 4.362631942911725 chr22 51304566 18799587 0.36643106970245104 1.2736235188222083 chrMT 16571 3078509 185.77689940257076 130.87077666472422 chrX 155270560 145304703 0.9358161843429946 4.321542180853495 chrY 59373566 11790448 0.19858076235474892 17.31814162089652