BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618658.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 38,523,005 number of mapped reads = 35,553,418 (92.29%) number of supplementary alignments = 117,620 (0.31%) number of secondary alignments = 0 number of mapped bases = 3,473,142,470 bp number of sequenced bases = 3,470,712,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,301,884 duplication rate = 23.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4051 >>>>>>> ACTG content number of A's = 951,710,963 bp (27.42%) number of C's = 762,744,008 bp (21.98%) number of T's = 966,985,780 bp (27.86%) number of G's = 754,686,760 bp (21.74%) number of N's = 34,585,051 bp (1%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0195 number of mismatches = 66,814,527 number of insertions = 653,749 mapped reads with insertion percentage = 1.81% number of deletions = 1,738,717 mapped reads with deletion percentage = 4.77% homopolymer indels = 53.03% >>>>>>> Coverage mean coverageData = 1.1219X std coverageData = 4.7479X There is a 24.8% of reference with a coverageData >= 1X There is a 16.32% of reference with a coverageData >= 2X There is a 11.79% of reference with a coverageData >= 3X There is a 8.94% of reference with a coverageData >= 4X There is a 7% of reference with a coverageData >= 5X There is a 5.61% of reference with a coverageData >= 6X There is a 4.59% of reference with a coverageData >= 7X There is a 3.82% of reference with a coverageData >= 8X There is a 3.21% of reference with a coverageData >= 9X There is a 2.73% of reference with a coverageData >= 10X There is a 2.35% of reference with a coverageData >= 11X There is a 2.03% of reference with a coverageData >= 12X There is a 1.77% of reference with a coverageData >= 13X There is a 1.55% of reference with a coverageData >= 14X There is a 1.36% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.07% of reference with a coverageData >= 17X There is a 0.96% of reference with a coverageData >= 18X There is a 0.86% of reference with a coverageData >= 19X There is a 0.77% of reference with a coverageData >= 20X There is a 0.69% of reference with a coverageData >= 21X There is a 0.63% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.52% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.43% of reference with a coverageData >= 26X There is a 0.39% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 307729943 1.2346205669032215 4.759153879079211 chr2 243199373 290150109 1.1930545108765556 6.46203247814488 chr3 198022430 223350073 1.127902899686667 3.615423975342916 chr4 191154276 177250250 0.9272628042074246 3.8438252235919137 chr5 180915260 198207694 1.0955830591626157 3.6227431478881047 chr6 171115067 189010130 1.1045791192659848 3.8027140687560137 chr7 159138663 172885556 1.0863831123175893 3.718846386172369 chr8 146364022 168522921 1.1513958054527909 3.752251872893013 chr9 141213431 148235546 1.049726962586158 4.037919879423622 chr10 135534747 173568456 1.2806196185248349 4.161426040507396 chr11 135006516 178459183 1.321856072487642 4.540871503558003 chr12 133851895 156629788 1.170172361026342 4.111057367901927 chr13 115169878 95636837 0.8303980056312988 3.1125707286466793 chr14 107349540 104239894 0.9710325167671887 3.454824960540854 chr15 102531392 114174920 1.1135606156600313 3.9020227947791333 chr16 90354753 119782328 1.3256892860965488 12.526941886614116 chr17 81195210 107105994 1.319117149890985 4.433892965040316 chr18 78077248 86674202 1.1101083122192013 4.180976914467358 chr19 59128983 73081391 1.2359656346533137 4.654645685827826 chr20 63025520 102124417 1.6203661151863562 4.9878874762910455 chr21 48129895 44422686 0.9229749202652531 6.2540297402300915 chr22 51304566 57890091 1.1283613821038851 4.350499527364444 chrMT 16571 3924 0.23679922756623017 0.7692473057556781 chrX 155270560 178487204 1.1495237989738685 3.7088372101124802 chrY 59373566 5518933 0.09295269548067907 3.4500437992168003