BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173998.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,981,828 number of mapped reads = 4,888,536 (98.13%) number of supplementary alignments = 568,755 (11.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,445,197 number of mapped paired reads (second in pair) = 2,443,339 number of mapped paired reads (both in pair) = 4,833,134 number of mapped paired reads (singletons) = 55,402 number of mapped bases = 550,451,891 bp number of sequenced bases = 550,052,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,967,453 duplication rate = 65.91% >>>>>>> Insert size mean insert size = 881,946.1155 std insert size = 8,931,334.6389 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 52.9467 >>>>>>> ACTG content number of A's = 165,346,056 bp (30.06%) number of C's = 108,578,701 bp (19.74%) number of T's = 163,820,378 bp (29.78%) number of G's = 112,303,238 bp (20.42%) number of N's = 4,316 bp (0%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 4,473,629 number of insertions = 57,344 mapped reads with insertion percentage = 1.13% number of deletions = 170,947 mapped reads with deletion percentage = 3.42% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 0.1778X std coverageData = 3.2111X There is a 3.52% of reference with a coverageData >= 1X There is a 2.67% of reference with a coverageData >= 2X There is a 2% of reference with a coverageData >= 3X There is a 1.66% of reference with a coverageData >= 4X There is a 1.27% of reference with a coverageData >= 5X There is a 1.09% of reference with a coverageData >= 6X There is a 0.84% of reference with a coverageData >= 7X There is a 0.75% of reference with a coverageData >= 8X There is a 0.57% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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% 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 46686503 0.18730746913565363 1.6373584933754783 chr2 243199373 53199891 0.21875011577435274 10.251176499794962 chr3 198022430 37097788 0.18734134309936507 1.3897058231433572 chr4 191154276 35662502 0.18656397725573243 1.5704643020779532 chr5 180915260 35590599 0.19672524584161669 1.4361849028464206 chr6 171115067 33997987 0.19868494105197645 1.5070121465535224 chr7 159138663 29149615 0.1831711694096613 1.556432962419776 chr8 146364022 25913312 0.177047006811551 1.910512259534697 chr9 141213431 23053101 0.1632500594083009 1.468410191108692 chr10 135534747 27742958 0.20469258706034993 1.9528283862997398 chr11 135006516 24413408 0.18083133113367655 1.3796296710540619 chr12 133851895 23122903 0.17274991138526652 1.3525503888765382 chr13 115169878 16561249 0.14379844181132154 1.2126441780642392 chr14 107349540 16885862 0.15729794463953922 1.2809418543468396 chr15 102531392 16141203 0.15742693710819805 1.2684718361415774 chr16 90354753 16702933 0.18485948381708264 1.5117327340007496 chr17 81195210 14836490 0.1827261731326269 1.399460161588357 chr18 78077248 20713346 0.2652929826625037 1.988079337639307 chr19 59128983 9518166 0.16097293606419716 1.3365658102314741 chr20 63025520 12457733 0.19766172496474443 1.421922137788628 chr21 48129895 7597130 0.15784638632600384 1.4265660839313903 chr22 51304566 6772916 0.13201390301206328 1.2899761793184679 chrMT 16571 669669 40.41210548548669 36.078909079925694 chrX 155270560 12339221 0.0794691601550223 0.8938541247358607 chrY 59373566 3625406 0.06106094419189846 0.9984743897505005