BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013201.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 = 2,279,733 number of mapped reads = 2,073,799 (90.97%) number of supplementary alignments = 16,234 (0.71%) number of secondary alignments = 0 number of mapped bases = 142,798,442 bp number of sequenced bases = 142,733,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,840 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2994 >>>>>>> ACTG content number of A's = 40,735,468 bp (28.54%) number of C's = 26,729,066 bp (18.73%) number of T's = 45,034,432 bp (31.55%) number of G's = 30,203,328 bp (21.16%) number of N's = 31,058 bp (0.02%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,098,000 number of insertions = 10,617 mapped reads with insertion percentage = 0.51% number of deletions = 37,614 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.4321X There is a 3.88% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 9699321 0.03891392912517558 0.8072317938477389 chr2 243199373 10607114 0.04361489040516564 0.41362532423344334 chr3 198022430 14245158 0.07193709318686776 0.30475446911003956 chr4 191154276 8686281 0.04544120687104065 0.2702357720923486 chr5 180915260 7905189 0.04369553458342873 0.23805751924289176 chr6 171115067 10158977 0.05936927225701288 0.3388110928585341 chr7 159138663 6974500 0.04382655898020207 0.6990850384372702 chr8 146364022 9871785 0.06744680055321245 0.5941057660685692 chr9 141213431 5154024 0.03649811468712208 0.3320729246932558 chr10 135534747 6414433 0.047326852648347066 0.4412282679202596 chr11 135006516 4872294 0.03608932475525848 0.2918309724460463 chr12 133851895 5703548 0.04261088720484682 0.24386277808629053 chr13 115169878 4105820 0.035650120251060784 0.21541282470556009 chr14 107349540 5193800 0.04838213559182461 0.262246285807419 chr15 102531392 3037478 0.029624858696934497 0.1941404617683813 chr16 90354753 4089893 0.04526483515482578 0.2660340411555803 chr17 81195210 2706039 0.03332756944652277 0.2172019537521971 chr18 78077248 4160624 0.053288558531161344 0.6814131767700276 chr19 59128983 2838587 0.048006694111414026 0.5600134024871994 chr20 63025520 2343262 0.037179574242306924 0.23454299078017346 chr21 48129895 1952156 0.04056015497228905 0.24893049296661618 chr22 51304566 2119009 0.041302542155799545 0.23052258998237737 chrMT 16571 419759 25.33093959326534 13.849636673009519 chrX 155270560 9221175 0.05938778735646989 0.3067659639846533 chrY 59373566 318216 0.005359556810180476 0.1427891714269244