BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089716.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 = 21,954,616 number of mapped reads = 19,081,921 (86.92%) number of supplementary alignments = 816 (0%) number of secondary alignments = 0 number of mapped bases = 904,039,926 bp number of sequenced bases = 903,870,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,971,982 duplication rate = 11.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6225 >>>>>>> ACTG content number of A's = 265,949,985 bp (29.42%) number of C's = 184,078,938 bp (20.37%) number of T's = 265,625,380 bp (29.39%) number of G's = 187,748,653 bp (20.77%) number of N's = 467,119 bp (0.05%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 4,631,679 number of insertions = 36,282 mapped reads with insertion percentage = 0.19% number of deletions = 112,059 mapped reads with deletion percentage = 0.59% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.292X std coverageData = 2.1413X There is a 11% of reference with a coverageData >= 1X There is a 6.21% of reference with a coverageData >= 2X There is a 3.85% of reference with a coverageData >= 3X There is a 2.48% of reference with a coverageData >= 4X There is a 1.62% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% 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 71185429 0.28559779997498985 4.29218626723938 chr2 243199373 76303759 0.313749817932302 2.0306693338554718 chr3 198022430 62493894 0.3155899763476289 1.2007869336297403 chr4 191154276 60799097 0.318062971293407 1.4037167976284344 chr5 180915260 56640318 0.31307650885834615 1.214808703800874 chr6 171115067 53547103 0.312930380350434 1.3382563414104294 chr7 159138663 48878229 0.30714238814485956 2.6066464301347096 chr8 146364022 46861896 0.32017360113266086 3.160650375103507 chr9 141213431 37360481 0.2645674758798262 1.7846024675447918 chr10 135534747 41855136 0.30881480156523994 1.8682096630186285 chr11 135006516 42225823 0.3127687777677338 1.9798800362315747 chr12 133851895 41005039 0.30634634646001835 1.309162237853846 chr13 115169878 29207582 0.2536043495678618 1.07734996600806 chr14 107349540 27082205 0.2522805873224981 1.182076401204285 chr15 102531392 24819119 0.24206361111336516 1.05481249881537 chr16 90354753 23617024 0.26138109192772624 1.1985409351275287 chr17 81195210 21696110 0.26720923561870213 1.4503378077408569 chr18 78077248 24302936 0.31126783566961785 3.909141492441116 chr19 59128983 15710046 0.2656911247737848 2.9173559441134587 chr20 63025520 17907368 0.2841288417771087 1.2663325889124126 chr21 48129895 11864578 0.24651161196175475 1.379732921360562 chr22 51304566 9675635 0.18859208359739366 0.9307434974064855 chrMT 16571 98576 5.948705569971637 5.613956189377918 chrX 155270560 55882241 0.3599023601125674 1.5904214473424645 chrY 59373566 3020302 0.05086947278861438 1.3418829923019289