BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524426.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 = 2,723,030 number of mapped reads = 2,507,446 (92.08%) number of supplementary alignments = 10,751 (0.39%) number of secondary alignments = 0 number of mapped bases = 146,807,151 bp number of sequenced bases = 146,765,245 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,636 duplication rate = 4.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.527 >>>>>>> ACTG content number of A's = 34,268,637 bp (23.35%) number of C's = 29,375,722 bp (20.02%) number of T's = 47,889,255 bp (32.63%) number of G's = 35,216,685 bp (24%) number of N's = 14,946 bp (0.01%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 733,929 number of insertions = 11,291 mapped reads with insertion percentage = 0.45% number of deletions = 26,106 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.06% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.4463X There is a 3.94% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12344654 0.04952707419733971 0.9549745922005289 chr2 243199373 11815084 0.048581885118593626 0.5734766065707058 chr3 198022430 10009761 0.05054862219396055 0.2657079401385788 chr4 191154276 9820123 0.05137276133964171 0.33832188917585787 chr5 180915260 9081853 0.05019948565975032 0.2618043728963005 chr6 171115067 5704344 0.03333630462827683 0.2360548682583471 chr7 159138663 8458112 0.05314932173333642 0.5823698656904527 chr8 146364022 7669359 0.05239920914444398 0.3494946164410785 chr9 141213431 5284550 0.037422431864855686 0.29179863118084487 chr10 135534747 7456785 0.05501751517638499 0.4629403067626092 chr11 135006516 5957818 0.04412985518417496 0.32667467979549913 chr12 133851895 6960924 0.05200467277657892 0.27706997465920136 chr13 115169878 4769538 0.0414130680940723 0.2388880059976132 chr14 107349540 4018305 0.03743197222829273 0.2376523495499478 chr15 102531392 4488823 0.0437799869136664 0.24670261623433798 chr16 90354753 4681178 0.05180887385083107 0.2891855037065901 chr17 81195210 4138975 0.05097560558067403 0.29741137521995104 chr18 78077248 4029901 0.05161428076973205 0.5474690297996756 chr19 59128983 4295910 0.07265320291404302 0.6570484383340538 chr20 63025520 4110475 0.06521921596204204 0.32333407655208374 chr21 48129895 2036872 0.042320308407072155 0.3224380412382789 chr22 51304566 1052509 0.02051491869164238 0.17022967600446573 chrMT 16571 19730 1.1906342405407035 1.3950260884109975 chrX 155270560 8101512 0.05217674232642685 0.30047058009367955 chrY 59373566 500056 0.008422199198882546 0.2557422840554737