BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234125.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 = 2,424,356 number of mapped reads = 1,165,349 (48.07%) number of supplementary alignments = 6,861 (0.28%) number of secondary alignments = 0 number of mapped bases = 82,698,231 bp number of sequenced bases = 82,683,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 654,960 duplication rate = 10.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.551 >>>>>>> ACTG content number of A's = 10,722,055 bp (12.97%) number of C's = 8,103,242 bp (9.8%) number of T's = 11,459,667 bp (13.86%) number of G's = 52,384,845 bp (63.36%) number of N's = 13,755 bp (0.02%) GC percentage = 73.16% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 358,716 number of insertions = 4,115 mapped reads with insertion percentage = 0.35% number of deletions = 8,622 mapped reads with deletion percentage = 0.73% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 87.9918X There is a 0.52% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 3276624 0.01314590104872798 0.254997203031123 chr2 243199373 46831561 0.19256448083030214 313.9334637745794 chr3 198022430 2051197 0.010358407378396477 0.21834424708267713 chr4 191154276 1568350 0.00820462943763811 0.18842096753310722 chr5 180915260 1667204 0.009215386253210481 0.21550753388853455 chr6 171115067 2342106 0.01368731603278395 0.26522690096563534 chr7 159138663 2146924 0.013490901327982125 0.2890955517681054 chr8 146364022 2545153 0.017389198282621667 0.2804386122854177 chr9 141213431 1641035 0.011620955516617962 0.22486244699923205 chr10 135534747 1878231 0.013857929730742773 0.2520852195014628 chr11 135006516 2391943 0.01771724114412374 0.35491681330523234 chr12 133851895 1156715 0.008641752886651324 0.20018354123573429 chr13 115169878 1833534 0.01592025651012672 0.2610883793693363 chr14 107349540 1693352 0.01577418962391455 0.7476212022677977 chr15 102531392 835277 0.008146548912551583 0.20470257547945106 chr16 90354753 736336 0.0081493886658071 0.19576173787071816 chr17 81195210 1143594 0.014084500797522416 0.25633704829894416 chr18 78077248 745045 0.009542408564400221 0.24234550679558975 chr19 59128983 1423580 0.024075841115007848 0.3337325263907832 chr20 63025520 1605824 0.02547894884484888 0.34100081427155554 chr21 48129895 1230606 0.02556843309132505 0.33600066201227763 chr22 51304566 520655 0.010148317013343412 0.20034575154979378 chrMT 16571 68606 4.140124313559833 4.704160573418699 chrX 155270560 1255759 0.008087553751335732 0.1897823864766871 chrY 59373566 109020 0.001836170662210183 0.07063110857262439