BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230332.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 = 3,348,137 number of mapped reads = 2,803,343 (83.73%) number of supplementary alignments = 22,045 (0.66%) number of secondary alignments = 0 number of mapped bases = 185,582,642 bp number of sequenced bases = 185,502,403 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,236 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8576 >>>>>>> ACTG content number of A's = 51,459,842 bp (27.74%) number of C's = 32,356,112 bp (17.44%) number of T's = 62,121,383 bp (33.49%) number of G's = 39,206,945 bp (21.14%) number of N's = 358,121 bp (0.19%) GC percentage = 38.58% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 2,073,166 number of insertions = 17,112 mapped reads with insertion percentage = 0.61% number of deletions = 48,895 mapped reads with deletion percentage = 1.73% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.581X There is a 4.82% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 24149416 0.09688808759276872 1.1544411762090594 chr2 243199373 11044485 0.04541329553509992 0.4611453879196351 chr3 198022430 7469382 0.03771987850063248 0.23402662723925732 chr4 191154276 11265980 0.058936583767553286 0.3317091990739463 chr5 180915260 9375723 0.05182383730371888 0.2746964668946317 chr6 171115067 10293917 0.0601578644152943 0.34622719214922193 chr7 159138663 10672392 0.06706347658582502 0.8239967185692337 chr8 146364022 15307590 0.1045857430728434 1.126310378959134 chr9 141213431 8030614 0.056868627460797266 0.4485147460764463 chr10 135534747 9626012 0.07102246629050778 0.489468203036919 chr11 135006516 9412593 0.06971954598102509 0.47328578329469234 chr12 133851895 9782612 0.07308534556047937 0.326424523495354 chr13 115169878 5904402 0.051266894630208774 0.2691510960811724 chr14 107349540 4248783 0.03957895860569128 0.2662835724001141 chr15 102531392 4804607 0.04685986317244186 0.2538036682684531 chr16 90354753 2646007 0.02928464648672107 0.24996074545736952 chr17 81195210 3938856 0.048510940485282324 0.3027250396540495 chr18 78077248 5845964 0.07487410416924531 0.8462202265814627 chr19 59128983 3011602 0.05093275492324974 0.6204492920455312 chr20 63025520 3144122 0.049886490424831086 0.2949848372963447 chr21 48129895 2426693 0.05041966121056362 0.31518729310390203 chr22 51304566 1565261 0.03050919483462739 0.2079652510349648 chrMT 16571 796833 48.085993603282844 23.665840392633957 chrX 155270560 10328512 0.0665194483745019 0.34057366528056643 chrY 59373566 490284 0.00825761417126268 0.19567203529063062