BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867840.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 = 17,404,735 number of mapped reads = 16,046,313 (92.2%) number of supplementary alignments = 35,988 (0.21%) number of secondary alignments = 0 number of mapped bases = 1,430,784,007 bp number of sequenced bases = 1,430,403,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 906,684 duplication rate = 1.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.3532 >>>>>>> ACTG content number of A's = 397,528,675 bp (27.79%) number of C's = 312,735,226 bp (21.86%) number of T's = 402,496,897 bp (28.14%) number of G's = 316,951,259 bp (22.16%) number of N's = 691,099 bp (0.05%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 6,471,914 number of insertions = 146,267 mapped reads with insertion percentage = 0.89% number of deletions = 150,401 mapped reads with deletion percentage = 0.91% homopolymer indels = 35.38% >>>>>>> Coverage mean coverageData = 0.4622X std coverageData = 6.491X There is a 33.13% of reference with a coverageData >= 1X There is a 8.23% of reference with a coverageData >= 2X There is a 1.76% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 135256219 0.5426514825012211 10.37974283959755 chr2 243199373 115410059 0.4745491634141672 3.2898578785363775 chr3 198022430 91576980 0.46245761149380904 4.5105288114652975 chr4 191154276 78195543 0.409070331233396 3.745506474404575 chr5 180915260 66756627 0.3689938980271758 0.7267668909560405 chr6 171115067 76576334 0.4475136838768266 1.552118527510877 chr7 159138663 90689952 0.5698800674227105 5.4376885583251084 chr8 146364022 77195187 0.5274191426633521 2.105330338124066 chr9 141213431 52072153 0.3687478778134071 2.3853756542084565 chr10 135534747 99559893 0.7345709879105762 23.493314964689255 chr11 135006516 65007652 0.48151492184273537 1.7267062410055238 chr12 133851895 61817355 0.46183399196552277 0.9803793993290288 chr13 115169878 39536580 0.3432892409593418 0.66388886386406 chr14 107349540 42471338 0.39563595708002103 0.8881626808615216 chr15 102531392 38662694 0.37708152835767605 0.6840402795797756 chr16 90354753 53272642 0.589594240825383 6.85514288614112 chr17 81195210 34947720 0.4304160306993479 1.6549010922574237 chr18 78077248 31908082 0.408673241147024 4.994283425912581 chr19 59128983 33275487 0.5627610236421621 6.372255716648022 chr20 63025520 30497236 0.483887098432508 1.3199600101584945 chr21 48129895 19962330 0.41475947537388147 2.8766115613612544 chr22 51304566 19020055 0.37072830905537724 0.7457959102868403 chrMT 16571 3075917 185.6204815641784 60.6102242606873 chrX 155270560 67139354 0.43240234336760297 1.3173800141685752 chrY 59373566 6900618 0.1162237417237159 5.453122192641003