BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716231.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 = 1,622,632 number of mapped reads = 1,442,422 (88.89%) number of supplementary alignments = 5,914 (0.36%) number of secondary alignments = 0 number of mapped bases = 81,891,549 bp number of sequenced bases = 81,867,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,544 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4252 >>>>>>> ACTG content number of A's = 20,445,209 bp (24.97%) number of C's = 16,427,225 bp (20.07%) number of T's = 26,279,468 bp (32.1%) number of G's = 18,714,288 bp (22.86%) number of N's = 1,235 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 443,877 number of insertions = 6,471 mapped reads with insertion percentage = 0.45% number of deletions = 14,273 mapped reads with deletion percentage = 0.98% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2518X There is a 2.4% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 6468857 0.025953223201798964 0.41784711923355383 chr2 243199373 7083075 0.029124561106495944 0.28907247643560136 chr3 198022430 5483570 0.02769166099012117 0.17978840710359129 chr4 191154276 5344226 0.027957658661007405 0.19923201735025045 chr5 180915260 5041280 0.027865421634416025 0.18277388490854735 chr6 171115067 4724208 0.027608369518974038 0.19677486363698515 chr7 159138663 4482466 0.02816704574173782 0.281514285834048 chr8 146364022 4141791 0.02829787637292449 0.26754957799249235 chr9 141213431 3437146 0.02434007852978234 0.2537333930269528 chr10 135534747 3847129 0.02838481706834927 0.2646389462362999 chr11 135006516 3740571 0.027706596028298367 0.2412855233287915 chr12 133851895 3758652 0.02808067827504422 0.19094111548924028 chr13 115169878 2582575 0.022424049107701582 0.15990710651992987 chr14 107349540 2490667 0.02320146877201337 0.1800713004745782 chr15 102531392 2301098 0.022442863157461083 0.16307823194784055 chr16 90354753 2302888 0.025487181620650327 0.1885140668197425 chr17 81195210 2165982 0.026676228807093423 0.18928669071913679 chr18 78077248 2258128 0.02892171609327214 0.44422189354146635 chr19 59128983 1639374 0.0277253880723773 0.3471445141684852 chr20 63025520 1677334 0.026613568598878676 0.1845724811195665 chr21 48129895 1093378 0.022717232190097237 0.1820548019983055 chr22 51304566 952403 0.01856370834517926 0.1467181825188626 chrMT 16571 11940 0.7205358759278258 0.9785966903167065 chrX 155270560 4597147 0.029607331872828952 0.2255330606669449 chrY 59373566 265664 0.00447444911764269 0.11713355300078888