BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716331.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,796,052 number of mapped reads = 1,571,430 (87.49%) number of supplementary alignments = 6,446 (0.36%) number of secondary alignments = 0 number of mapped bases = 89,743,557 bp number of sequenced bases = 89,719,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,689 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7471 >>>>>>> ACTG content number of A's = 22,755,800 bp (25.36%) number of C's = 15,925,949 bp (17.75%) number of T's = 29,314,854 bp (32.67%) number of G's = 21,721,305 bp (24.21%) number of N's = 1,406 bp (0%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 486,186 number of insertions = 5,583 mapped reads with insertion percentage = 0.35% number of deletions = 14,498 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.2589X There is a 2.61% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7276072 0.02919179086017202 0.44245367209433367 chr2 243199373 7309675 0.030056306929705776 0.2776928841844122 chr3 198022430 6062911 0.030617294212579856 0.1896642170914894 chr4 191154276 5958452 0.03117090616377318 0.21193402100807118 chr5 180915260 5392285 0.02980558411711649 0.18840424065128264 chr6 171115067 5213192 0.03046600215514628 0.20459597489278997 chr7 159138663 4942734 0.031059290726854982 0.29859333108898417 chr8 146364022 4644211 0.03173055055838791 0.2813957144480666 chr9 141213431 3839339 0.02718819996661649 0.25469538606556924 chr10 135534747 4225283 0.031174906018749567 0.2771278446029752 chr11 135006516 4157803 0.030797054269587995 0.2358248615861339 chr12 133851895 4126686 0.030830239646588493 0.19639262638178265 chr13 115169878 2909303 0.025260971449496544 0.1707561937242555 chr14 107349540 2776110 0.025860474111020878 0.18954666352512153 chr15 102531392 2565199 0.02501866940419574 0.17120106748998462 chr16 90354753 2523207 0.027925559156804954 0.20042726770415611 chr17 81195210 2291500 0.028222108176085756 0.19330043032278915 chr18 78077248 2369134 0.030343461900706338 0.4381399421568576 chr19 59128983 1639358 0.027725117477498302 0.33826157249021616 chr20 63025520 1875128 0.029751884633399298 0.1951819904834867 chr21 48129895 1252982 0.026033341647639166 0.1937295891601855 chr22 51304566 999894 0.019489376442634754 0.1513101205010626 chrMT 16571 21744 1.3121718665137891 1.430837881003601 chrX 155270560 5098495 0.03283619895490813 0.22298214346845902 chrY 59373566 272860 0.004595647834256747 0.1156452165017821