BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,233,914 number of mapped reads = 994,487 (80.6%) number of supplementary alignments = 11,196 (0.91%) number of secondary alignments = 0 number of mapped bases = 65,449,552 bp number of sequenced bases = 65,421,577 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,730 duplication rate = 8.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1861 >>>>>>> ACTG content number of A's = 17,671,529 bp (27.01%) number of C's = 12,646,377 bp (19.33%) number of T's = 20,188,888 bp (30.86%) number of G's = 14,906,676 bp (22.79%) number of N's = 8,107 bp (0.01%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 526,054 number of insertions = 4,574 mapped reads with insertion percentage = 0.45% number of deletions = 16,229 mapped reads with deletion percentage = 1.61% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.3369X There is a 1.2% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 6984084 0.028020327379645726 0.4342248941782502 chr2 243199373 4472150 0.018388822079734555 0.6595126911115029 chr3 198022430 3076448 0.015535856215884231 0.2006971139455658 chr4 191154276 2693881 0.014092705935597277 0.1883004099552644 chr5 180915260 2769017 0.015305602191877014 0.19744966584319545 chr6 171115067 2925299 0.01709550801858962 0.2205956678244245 chr7 159138663 2348817 0.014759562231586676 0.24940933855606848 chr8 146364022 2271552 0.015519879605385537 0.36439461658815797 chr9 141213431 1919109 0.013590130814114983 0.38412482281617666 chr10 135534747 4607407 0.033994286350790916 0.327422500982283 chr11 135006516 2531756 0.018752843010925488 0.2990743080279841 chr12 133851895 1992581 0.014886460890224976 0.19905483008089553 chr13 115169878 1375355 0.011941968020492303 0.17507689829496142 chr14 107349540 1915007 0.017838986548056004 0.22338779709407247 chr15 102531392 1325446 0.012927221352851622 0.1951346770417553 chr16 90354753 1374088 0.015207700252359718 0.20028963848096995 chr17 81195210 1185968 0.014606378873827656 0.20724076231494715 chr18 78077248 9336492 0.11958018807220254 0.6175847466940937 chr19 59128983 1022342 0.01729003186136315 0.3520429175743758 chr20 63025520 3681593 0.05841432169064214 0.41612341708878253 chr21 48129895 620631 0.0128949169741592 0.18219797964395637 chr22 51304566 524519 0.010223631947300752 0.16651603890987945 chrMT 16571 21164 1.2771709613179651 1.8461529022039327 chrX 155270560 4317798 0.02780822069553945 0.29874737473185675 chrY 59373566 157048 0.0026450828302952193 0.08705734784646262