BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818891.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,177,382 number of mapped reads = 1,161,759 (98.67%) number of supplementary alignments = 16,353 (1.39%) number of secondary alignments = 0 number of mapped bases = 107,583,113 bp number of sequenced bases = 107,514,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,057 duplication rate = 12.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1669 >>>>>>> ACTG content number of A's = 30,489,957 bp (28.36%) number of C's = 23,888,166 bp (22.22%) number of T's = 29,668,295 bp (27.59%) number of G's = 23,466,227 bp (21.83%) number of N's = 1,572 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 667,216 number of insertions = 14,766 mapped reads with insertion percentage = 1.22% number of deletions = 34,899 mapped reads with deletion percentage = 2.93% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 0.4737X There is a 2.71% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 10214055 0.0409790553741489 0.7179397052569185 chr2 243199373 8226848 0.03382758721174828 0.699973757284212 chr3 198022430 6611558 0.03338792479215612 0.22144141963145886 chr4 191154276 5370189 0.02809348089079629 0.2698683492504886 chr5 180915260 4719630 0.026087517437721947 0.20812509497879028 chr6 171115067 5263773 0.03076159856805596 0.23404792145260345 chr7 159138663 9593181 0.06028190019417217 1.0291181677045216 chr8 146364022 9323360 0.063699807320135 0.3797359679121767 chr9 141213431 3990720 0.02826020139684872 0.38667480909827084 chr10 135534747 5044844 0.03722177605127341 0.6593310405151894 chr11 135006516 4718150 0.0349475724564287 0.27720962307519104 chr12 133851895 4182691 0.031248649860354985 0.21614738903643416 chr13 115169878 3231585 0.028059289947324595 0.20045620265596967 chr14 107349540 3156027 0.029399539113069324 0.23107104999384914 chr15 102531392 2989546 0.029157372602529378 0.2064298750738702 chr16 90354753 2747060 0.03040304918989707 0.48107369282048373 chr17 81195210 2760560 0.033999049943956056 0.3030585759096084 chr18 78077248 2054580 0.026314708223322627 0.4223963167795031 chr19 59128983 1941341 0.03283230831147561 0.611106232388143 chr20 63025520 4440793 0.07046023579020054 0.34571197282465566 chr21 48129895 1042756 0.021665453456734114 0.20895443663605304 chr22 51304566 1018187 0.019845933400937453 0.18490035640125904 chrMT 16571 167478 10.106692414458994 6.804323319428971 chrX 155270560 4361076 0.02808694706839468 0.2423532064877227 chrY 59373566 413125 0.006958062785044779 0.5402881528027028