BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618566.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 = 267,348,940 number of mapped reads = 256,145,362 (95.81%) number of supplementary alignments = 2,903,577 (1.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 128,961,928 number of mapped paired reads (second in pair) = 127,183,434 number of mapped paired reads (both in pair) = 252,122,158 number of mapped paired reads (singletons) = 4,023,204 number of mapped bases = 24,006,018,404 bp number of sequenced bases = 23,989,661,140 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,459,595 duplication rate = 32% >>>>>>> Insert size mean insert size = 155,967.4514 std insert size = 3,900,614.2312 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.443 >>>>>>> ACTG content number of A's = 6,497,739,941 bp (27.09%) number of C's = 5,233,565,728 bp (21.82%) number of T's = 6,551,468,865 bp (27.31%) number of G's = 5,705,306,066 bp (23.78%) number of N's = 1,580,540 bp (0.01%) GC percentage = 45.6% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 326,299,746 number of insertions = 4,050,260 mapped reads with insertion percentage = 1.56% number of deletions = 11,929,585 mapped reads with deletion percentage = 4.54% homopolymer indels = 52.15% >>>>>>> Coverage mean coverageData = 7.7546X std coverageData = 26.3968X There is a 45.98% of reference with a coverageData >= 1X There is a 37.97% of reference with a coverageData >= 2X There is a 32.92% of reference with a coverageData >= 3X There is a 29.27% of reference with a coverageData >= 4X There is a 26.4% of reference with a coverageData >= 5X There is a 24.07% of reference with a coverageData >= 6X There is a 22.12% of reference with a coverageData >= 7X There is a 20.46% of reference with a coverageData >= 8X There is a 19.02% of reference with a coverageData >= 9X There is a 17.76% of reference with a coverageData >= 10X There is a 16.64% of reference with a coverageData >= 11X There is a 15.64% of reference with a coverageData >= 12X There is a 14.74% of reference with a coverageData >= 13X There is a 13.93% of reference with a coverageData >= 14X There is a 13.19% of reference with a coverageData >= 15X There is a 12.52% of reference with a coverageData >= 16X There is a 11.9% of reference with a coverageData >= 17X There is a 11.32% of reference with a coverageData >= 18X There is a 10.8% of reference with a coverageData >= 19X There is a 10.31% of reference with a coverageData >= 20X There is a 9.86% of reference with a coverageData >= 21X There is a 9.43% of reference with a coverageData >= 22X There is a 9.04% of reference with a coverageData >= 23X There is a 8.67% of reference with a coverageData >= 24X There is a 8.32% of reference with a coverageData >= 25X There is a 7.99% of reference with a coverageData >= 26X There is a 7.69% of reference with a coverageData >= 27X There is a 7.4% of reference with a coverageData >= 28X There is a 7.13% of reference with a coverageData >= 29X There is a 6.87% of reference with a coverageData >= 30X There is a 6.62% of reference with a coverageData >= 31X There is a 6.39% of reference with a coverageData >= 32X There is a 6.17% of reference with a coverageData >= 33X There is a 5.96% of reference with a coverageData >= 34X There is a 5.76% of reference with a coverageData >= 35X There is a 5.57% of reference with a coverageData >= 36X There is a 5.39% of reference with a coverageData >= 37X There is a 5.22% of reference with a coverageData >= 38X There is a 5.06% of reference with a coverageData >= 39X There is a 4.9% of reference with a coverageData >= 40X There is a 4.75% of reference with a coverageData >= 41X There is a 4.61% of reference with a coverageData >= 42X There is a 4.47% of reference with a coverageData >= 43X There is a 4.34% of reference with a coverageData >= 44X There is a 4.21% of reference with a coverageData >= 45X There is a 4.09% of reference with a coverageData >= 46X There is a 3.97% of reference with a coverageData >= 47X There is a 3.86% of reference with a coverageData >= 48X There is a 3.75% of reference with a coverageData >= 49X There is a 3.65% of reference with a coverageData >= 50X There is a 3.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2043224972 8.19747194130361 30.946933517457968 chr2 243199373 2014370233 8.28279369371565 28.864258970025745 chr3 198022430 1520619193 7.679025012469547 22.696257798639515 chr4 191154276 1228313501 6.425770465108507 23.09162644504342 chr5 180915260 1348405032 7.453240992495602 22.078166486823868 chr6 171115067 1327701466 7.759114900150785 23.8216543803731 chr7 159138663 1197806939 7.526812883931292 22.763121938590963 chr8 146364022 1172060118 8.007843061322816 23.189064373239997 chr9 141213431 1007243237 7.1327722148469 29.35249644541363 chr10 135534747 1173402861 8.657579602077982 25.941466804082076 chr11 135006516 1151508281 8.52927929048995 27.856677820840996 chr12 133851895 1080935627 8.075609441315716 24.003068926879433 chr13 115169878 608042705 5.279528949401162 16.95646266410467 chr14 107349540 761099444 7.0899180751030695 23.102951312014646 chr15 102531392 812699481 7.926347874024767 25.033758774221802 chr16 90354753 830041017 9.186467667063402 37.307908800251575 chr17 81195210 762508112 9.391047969455341 29.5715543533733 chr18 78077248 658052976 8.428229642520186 32.9257207053004 chr19 59128983 541137899 9.151821518729657 30.45910443159826 chr20 63025520 703213809 11.157604237140765 31.877607708459013 chr21 48129895 322119154 6.692704274547036 38.18158796518431 chr22 51304566 438113753 8.53946904063081 29.71599927572445 chrMT 16571 84307 5.087622955766097 12.02044956145221 chrX 155270560 1267042958 8.160226626348226 22.963878872413627 chrY 59373566 36271329 0.6109002952593415 14.404336236232282