BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618644.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 = 47,802,900 number of mapped reads = 42,433,358 (88.77%) number of supplementary alignments = 118,910 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,042,847 number of mapped paired reads (second in pair) = 19,390,511 number of mapped paired reads (both in pair) = 38,378,496 number of mapped paired reads (singletons) = 4,054,862 number of mapped bases = 3,960,421,463 bp number of sequenced bases = 3,957,626,607 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,304,021 duplication rate = 17% >>>>>>> Insert size mean insert size = 92,565.8874 std insert size = 3,058,211.7431 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.8672 >>>>>>> ACTG content number of A's = 1,076,361,479 bp (27.2%) number of C's = 877,273,976 bp (22.17%) number of T's = 1,092,827,174 bp (27.61%) number of G's = 909,951,770 bp (22.99%) number of N's = 1,212,208 bp (0.03%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.016 number of mismatches = 62,400,595 number of insertions = 722,703 mapped reads with insertion percentage = 1.67% number of deletions = 2,027,496 mapped reads with deletion percentage = 4.66% homopolymer indels = 52.5% >>>>>>> Coverage mean coverageData = 1.2793X std coverageData = 5.1971X There is a 27.73% of reference with a coverageData >= 1X There is a 18.21% of reference with a coverageData >= 2X There is a 13.13% of reference with a coverageData >= 3X There is a 10.03% of reference with a coverageData >= 4X There is a 7.91% of reference with a coverageData >= 5X There is a 6.39% of reference with a coverageData >= 6X There is a 5.26% of reference with a coverageData >= 7X There is a 4.39% of reference with a coverageData >= 8X There is a 3.71% of reference with a coverageData >= 9X There is a 3.16% of reference with a coverageData >= 10X There is a 2.72% of reference with a coverageData >= 11X There is a 2.35% of reference with a coverageData >= 12X There is a 2.05% of reference with a coverageData >= 13X There is a 1.8% of reference with a coverageData >= 14X There is a 1.58% of reference with a coverageData >= 15X There is a 1.4% of reference with a coverageData >= 16X There is a 1.24% of reference with a coverageData >= 17X There is a 1.11% of reference with a coverageData >= 18X There is a 0.99% of reference with a coverageData >= 19X There is a 0.89% of reference with a coverageData >= 20X There is a 0.8% of reference with a coverageData >= 21X There is a 0.72% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.59% of reference with a coverageData >= 24X There is a 0.54% of reference with a coverageData >= 25X There is a 0.49% of reference with a coverageData >= 26X There is a 0.45% of reference with a coverageData >= 27X There is a 0.41% of reference with a coverageData >= 28X There is a 0.38% of reference with a coverageData >= 29X There is a 0.35% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 361345028 1.4497256879452267 5.954792157266587 chr2 243199373 344147106 1.4150822091140836 6.706248818069613 chr3 198022430 265406938 1.3402872492777713 4.542344651347152 chr4 191154276 210636424 1.1019184525069166 4.304655064555826 chr5 180915260 233613196 1.2912851906467149 4.682513938598812 chr6 171115067 222509652 1.3003510205211795 4.39900112598991 chr7 159138663 208154589 1.308007652420707 4.49937815551207 chr8 146364022 202794968 1.385552031359182 4.991127079557013 chr9 141213431 175483239 1.2426809387557476 5.283768355666084 chr10 135534747 206510655 1.523673150767751 5.185831656884775 chr11 135006516 210150407 1.5565945498512086 5.49617809440559 chr12 133851895 184209845 1.3762214199507599 4.913691722158964 chr13 115169878 111962954 0.9721548372222814 3.6580604858484924 chr14 107349540 126556375 1.1789186520966928 4.3432825463519595 chr15 102531392 133370868 1.3007808184248586 4.890016755341026 chr16 90354753 143861961 1.592190296840278 8.938222644044101 chr17 81195210 132597628 1.633072049447252 5.315743189205022 chr18 78077248 102711590 1.3155124268724225 5.075352591769574 chr19 59128983 89832728 1.519267260186092 5.510269118486007 chr20 63025520 114935961 1.8236416137463047 5.755130138241796 chr21 48129895 53917988 1.120259830194934 6.70028406550774 chr22 51304566 72830879 1.4195788928416235 5.385854295419808 chrMT 16571 15035 0.907307947619335 2.1284746084934314 chrX 155270560 18320121 0.11798837461525225 2.0817756791434285 chrY 59373566 34545328 0.5818301026419737 4.2787131551711015