BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708518.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,128,577 number of mapped reads = 2,286,517 (73.08%) number of supplementary alignments = 461 (0.01%) number of secondary alignments = 0 number of mapped bases = 111,349,812 bp number of sequenced bases = 111,328,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,130 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7033 >>>>>>> ACTG content number of A's = 32,962,101 bp (29.61%) number of C's = 21,021,912 bp (18.88%) number of T's = 35,120,279 bp (31.55%) number of G's = 22,222,787 bp (19.96%) number of N's = 1,638 bp (0%) GC percentage = 38.84% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 551,466 number of insertions = 5,439 mapped reads with insertion percentage = 0.24% number of deletions = 13,724 mapped reads with deletion percentage = 0.6% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3549X There is a 3.07% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 8889343 0.035664276238653786 0.6320354178512276 chr2 243199373 9873316 0.040597621113110355 0.28993373852558163 chr3 198022430 7850529 0.03964464530608982 0.22938702420904564 chr4 191154276 7707039 0.04031842321957789 0.23253650567782866 chr5 180915260 7228948 0.03995764646940231 0.2288837727791648 chr6 171115067 6646055 0.038839683240751675 0.27188974414686773 chr7 159138663 6461416 0.04060242733093717 0.46119439363267545 chr8 146364022 5906900 0.040357595529863205 0.7600263351833931 chr9 141213431 4647499 0.032911168343470104 0.25909052228484114 chr10 135534747 5180408 0.03822199188522483 0.28601568262130683 chr11 135006516 5176896 0.038345526967009505 0.31681811401526483 chr12 133851895 5199478 0.038845008507350606 0.22725833730543712 chr13 115169878 3885088 0.03373354272373198 0.20897105474394914 chr14 107349540 3466899 0.03229542483367884 0.21129124998036042 chr15 102531392 3143358 0.030657518040913753 0.1989342116771856 chr16 90354753 2860766 0.03166148879849187 0.21094376410553684 chr17 81195210 2698607 0.033236036953411416 0.25515914758378155 chr18 78077248 3049739 0.03906053399832945 0.4398556623156145 chr19 59128983 1901542 0.03215922046215475 0.45150518779639826 chr20 63025520 2227671 0.03534553939420095 0.21878510531486914 chr21 48129895 1559230 0.032396289250163544 0.24781409602623627 chr22 51304566 1086787 0.02118304635887574 0.19112433646660423 chrMT 16571 131709 7.948162452477219 5.595554637363741 chrX 155270560 3774769 0.024310912512970906 0.20540031940011683 chrY 59373566 795820 0.013403607928821388 0.14473464892159044