BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053604.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 12,084,818 number of mapped reads = 8,619,490 (71.32%) number of supplementary alignments = 241 (0%) number of secondary alignments = 0 number of mapped bases = 407,250,464 bp number of sequenced bases = 407,169,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,434,714 duplication rate = 20.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2465 >>>>>>> ACTG content number of A's = 119,496,887 bp (29.35%) number of C's = 78,043,780 bp (19.17%) number of T's = 122,005,469 bp (29.96%) number of G's = 87,309,071 bp (21.44%) number of N's = 313,982 bp (0.08%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 2,752,273 number of insertions = 17,977 mapped reads with insertion percentage = 0.21% number of deletions = 54,282 mapped reads with deletion percentage = 0.63% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.1316X std coverageData = 1.0224X There is a 4.85% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 32051539 0.12859161141267528 1.0649432203338538 chr2 243199373 34512110 0.14190871289787413 1.177442037023103 chr3 198022430 27938750 0.1410888150397912 0.9832100060833721 chr4 191154276 27080386 0.14166769672471255 1.0184974054220157 chr5 180915260 25668796 0.14188297880455192 0.9917846511180184 chr6 171115067 23962285 0.14003609045134524 1.0418369308661157 chr7 159138663 22278137 0.13999198296645235 1.1603747127620063 chr8 146364022 20482804 0.13994425487979553 1.04984009580752 chr9 141213431 16858374 0.11938222788454166 0.9634583697755563 chr10 135534747 18733480 0.1382190206914246 1.050715340225078 chr11 135006516 18539180 0.13732063125012425 1.0561786955588097 chr12 133851895 18780354 0.1403069713730986 0.9782136876103231 chr13 115169878 13170334 0.11435571721279413 0.8987419901238131 chr14 107349540 12205996 0.11370329113659919 0.9976490993536978 chr15 102531392 11504858 0.11220815182144411 0.8676236333006663 chr16 90354753 11179629 0.12373039191419183 0.9585643018713631 chr17 81195210 10623996 0.13084510773480357 0.9377451631230518 chr18 78077248 10418225 0.13343483878939996 1.1124739599471716 chr19 59128983 7605067 0.1286182615385081 1.0506516382402498 chr20 63025520 8324228 0.13207710146619972 0.969589165032303 chr21 48129895 5054940 0.1050270315362209 0.9215436639189024 chr22 51304566 4366671 0.08511271686812437 0.7383473632155387 chrMT 16571 91355 5.512944300283628 10.332514458477688 chrX 155270560 24797098 0.15970250896242016 1.1202513856508922 chrY 59373566 1021872 0.017210891459677528 0.35851004268837106