BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716713.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 = 1,171,358 number of mapped reads = 1,089,730 (93.03%) number of supplementary alignments = 30,049 (2.57%) number of secondary alignments = 0 number of mapped bases = 83,156,485 bp number of sequenced bases = 83,124,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,688 duplication rate = 2.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2812 >>>>>>> ACTG content number of A's = 19,955,024 bp (24.01%) number of C's = 16,687,365 bp (20.08%) number of T's = 25,129,706 bp (30.23%) number of G's = 21,349,732 bp (25.68%) number of N's = 3,097 bp (0%) GC percentage = 45.76% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 548,590 number of insertions = 7,246 mapped reads with insertion percentage = 0.65% number of deletions = 15,295 mapped reads with deletion percentage = 1.38% homopolymer indels = 39.47% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.2421X There is a 2.35% of reference with a coverageData >= 1X There is a 0.24% 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% 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 9150279 0.036711158284335826 0.41288796684834 chr2 243199373 7063518 0.029044145603122094 0.25948058987785017 chr3 198022430 5414652 0.027343629709018318 0.1858510035514722 chr4 191154276 4083307 0.02136131655250024 0.2151589695270469 chr5 180915260 4280471 0.02366008815397883 0.17227269726810537 chr6 171115067 4736797 0.02768193989603499 0.19439492691442783 chr7 159138663 5273662 0.03313878538743285 0.32905854266166434 chr8 146364022 5261750 0.03594975000072081 0.267553514859173 chr9 141213431 2550821 0.018063586317083394 0.1740400566061748 chr10 135534747 4513185 0.03329909930772217 0.31575104117747926 chr11 135006516 3573285 0.026467500279764276 0.21457315531855933 chr12 133851895 2993271 0.022362559753076338 0.1662251551555804 chr13 115169878 1584770 0.013760282007071328 0.12798173192634213 chr14 107349540 1589190 0.014803882718081512 0.14204897620082368 chr15 102531392 1605254 0.015656219706838663 0.13745353444479858 chr16 90354753 2392533 0.02647932643897549 0.19068813983356436 chr17 81195210 2000867 0.024642672886738024 0.1883926154163269 chr18 78077248 2288986 0.029316940064280955 0.2625016076408178 chr19 59128983 2189243 0.037024871542268877 0.3253054061854485 chr20 63025520 2261203 0.03587757784465721 0.2190408239165077 chr21 48129895 1298320 0.026975334145233437 0.21422973315779578 chr22 51304566 1375422 0.026808958875122343 0.1912191813139398 chrMT 16571 12190 0.7356224729949913 0.9852194152224452 chrX 155270560 5387678 0.03469864473986569 0.2138699414848074 chrY 59373566 275831 0.004645686937516941 0.15688706183681586