BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234059.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 = 5,822,496 number of mapped reads = 5,055,965 (86.84%) number of supplementary alignments = 34,990 (0.6%) number of secondary alignments = 0 number of mapped bases = 329,434,060 bp number of sequenced bases = 329,240,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 361,697 duplication rate = 5.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9427 >>>>>>> ACTG content number of A's = 92,332,972 bp (28.04%) number of C's = 59,233,558 bp (17.99%) number of T's = 105,744,335 bp (32.12%) number of G's = 71,911,866 bp (21.84%) number of N's = 17,589 bp (0.01%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,480,354 number of insertions = 23,390 mapped reads with insertion percentage = 0.46% number of deletions = 111,340 mapped reads with deletion percentage = 2.18% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.1064X std coverageData = 0.9544X There is a 7.85% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 33181780 0.1331261678180533 2.3159798896643013 chr2 243199373 25388965 0.10439568444117658 0.8629564553031218 chr3 198022430 44456006 0.22449985085022944 0.6127006621129225 chr4 191154276 12031337 0.06294045444214913 0.367806916435004 chr5 180915260 19360354 0.10701338295066984 0.4260858282550361 chr6 171115067 20354178 0.11895023832121107 0.6315924221495088 chr7 159138663 15575534 0.09787397799113091 0.9370818560111585 chr8 146364022 16743507 0.11439633026755715 1.4438797197392004 chr9 141213431 11510146 0.08150886157563865 0.5955463197931155 chr10 135534747 14319709 0.10565341594653953 0.8800411446440898 chr11 135006516 12185528 0.09025881387828717 0.6595611102476379 chr12 133851895 11670464 0.08718938196579137 0.40503215983500546 chr13 115169878 12508175 0.10860630589536614 0.41775185820875665 chr14 107349540 17553954 0.16352146455401673 0.5514030472885904 chr15 102531392 6478787 0.0631883257763632 0.32403082170356906 chr16 90354753 9209543 0.10192649190242377 0.48955828981728555 chr17 81195210 8405523 0.10352239990511755 0.4873865022371825 chr18 78077248 5156100 0.066038444387794 1.3588318477782309 chr19 59128983 7569626 0.1280188769693536 1.3415226989189817 chr20 63025520 6535584 0.10369742288520586 0.45057124871307924 chr21 48129895 5469201 0.11363417684580446 0.4628034132033366 chr22 51304566 2466442 0.048074512510251036 0.2674955646493838 chrMT 16571 122901 7.416631464606843 5.103923157604584 chrX 155270560 10477143 0.06747668714532877 0.42784241279672663 chrY 59373566 703573 0.011849936720998029 0.23651136491781333