BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237809.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,221,608 number of mapped reads = 1,863,632 (83.89%) number of supplementary alignments = 10,297 (0.46%) number of secondary alignments = 0 number of mapped bases = 117,330,037 bp number of sequenced bases = 117,276,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,005 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9555 >>>>>>> ACTG content number of A's = 31,460,348 bp (26.83%) number of C's = 23,286,907 bp (19.86%) number of T's = 34,197,433 bp (29.16%) number of G's = 28,227,427 bp (24.07%) number of N's = 104,231 bp (0.09%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 937,985 number of insertions = 10,432 mapped reads with insertion percentage = 0.55% number of deletions = 31,527 mapped reads with deletion percentage = 1.67% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0379X std coverageData = 0.3701X There is a 3.4% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% 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 0.01% 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 11107006 0.04456159810330021 0.6844460618200753 chr2 243199373 12014775 0.04940298509733411 0.421103995871862 chr3 198022430 8554831 0.043201323203639105 0.23395162206983158 chr4 191154276 4909120 0.025681455328783753 0.23365126236212483 chr5 180915260 5640304 0.031176496664792126 0.19124945023264503 chr6 171115067 5421399 0.03168276818078212 0.2406553438171351 chr7 159138663 6392506 0.04016940873758629 0.5448919089856947 chr8 146364022 6856402 0.04684485918267537 0.32737851348930974 chr9 141213431 4602826 0.032594817415065855 0.32047650383521337 chr10 135534747 7178328 0.0529630088142637 0.5573560353397321 chr11 135006516 6849521 0.05073474379562539 0.37186114724900315 chr12 133851895 6324864 0.047252704192196904 0.2395002166751172 chr13 115169878 3108518 0.026990720611859986 0.1752028758334259 chr14 107349540 3341967 0.03113163782536935 0.2276592472699185 chr15 102531392 1997360 0.019480472868250925 0.15014738639883807 chr16 90354753 3278710 0.03628707833444025 0.2513916999477049 chr17 81195210 3218585 0.03964008467987212 0.26198538231252666 chr18 78077248 1605979 0.020569103562666554 0.5364686396197489 chr19 59128983 3232681 0.05467168275158732 0.5059010712599098 chr20 63025520 2430049 0.038556587871071905 0.22886837574531035 chr21 48129895 1619668 0.033652016070261526 0.2453557728373686 chr22 51304566 935514 0.018234517372196463 0.14376809987405392 chrMT 16571 47488 2.8657292861022268 2.4303052461039822 chrX 155270560 6279107 0.040439778152407 0.2559756207998156 chrY 59373566 382529 0.006442749286778564 0.1851546358817138