BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008678.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 = 1,102,839 number of mapped reads = 969,623 (87.92%) number of supplementary alignments = 6,376 (0.58%) number of secondary alignments = 0 number of mapped bases = 62,843,761 bp number of sequenced bases = 62,814,390 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,300 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5226 >>>>>>> ACTG content number of A's = 17,588,953 bp (28%) number of C's = 11,352,169 bp (18.07%) number of T's = 19,779,354 bp (31.49%) number of G's = 14,082,920 bp (22.42%) number of N's = 10,994 bp (0.02%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 466,935 number of insertions = 5,307 mapped reads with insertion percentage = 0.54% number of deletions = 18,125 mapped reads with deletion percentage = 1.85% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.2221X There is a 1.86% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5835846 0.02341356654032168 0.4067380738826137 chr2 243199373 6089473 0.02503901603397637 0.24299421677451807 chr3 198022430 4766456 0.024070283351234505 0.16592224935196204 chr4 191154276 3241824 0.016959202105424 0.1419965132404942 chr5 180915260 2720281 0.015036216403193407 0.13030675744867118 chr6 171115067 3321287 0.019409670102282693 0.1616576298483985 chr7 159138663 3419254 0.02148600431562002 0.2731488703433702 chr8 146364022 5093086 0.034797390304018835 0.3041624459844937 chr9 141213431 1813053 0.012839097436843666 0.18060093084353385 chr10 135534747 3487288 0.02572984476076825 0.23795331481185314 chr11 135006516 3044377 0.02254985233453473 0.24439558680031806 chr12 133851895 2946750 0.02201500397136701 0.15792619482004347 chr13 115169878 1937322 0.016821429644997974 0.13640495707187014 chr14 107349540 2354373 0.021931840602204725 0.16017841930128257 chr15 102531392 1310098 0.012777530612283114 0.11963712462994518 chr16 90354753 1473659 0.016309700940690966 0.1473109717589051 chr17 81195210 1784653 0.021979781812252224 0.1862762729403517 chr18 78077248 896915 0.011487533474540497 0.31209008865131765 chr19 59128983 1052172 0.017794522188890008 0.25679837791150756 chr20 63025520 1183046 0.018770904230540265 0.14811111016649037 chr21 48129895 615706 0.012792589719965107 0.12477873141154823 chr22 51304566 738311 0.014390746429859673 0.12586466038252028 chrMT 16571 51919 3.1331241325206687 2.405639478355637 chrX 155270560 3498028 0.022528597823051583 0.17594944735197438 chrY 59373566 168584 0.002839378049147326 0.08387833522910434