BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717056.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 = 829,549 number of mapped reads = 713,369 (85.99%) number of supplementary alignments = 2,950 (0.36%) number of secondary alignments = 0 number of mapped bases = 40,240,064 bp number of sequenced bases = 40,228,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,600 duplication rate = 1.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2972 >>>>>>> ACTG content number of A's = 9,350,846 bp (23.24%) number of C's = 8,528,620 bp (21.2%) number of T's = 11,288,185 bp (28.06%) number of G's = 11,059,821 bp (27.49%) number of N's = 1,065 bp (0%) GC percentage = 48.69% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 215,287 number of insertions = 2,785 mapped reads with insertion percentage = 0.39% number of deletions = 6,796 mapped reads with deletion percentage = 0.94% homopolymer indels = 36.74% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 0.1358X There is a 1.2% of reference with a coverageData >= 1X There is a 0.07% 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 3914150 0.01570367200810304 0.15499006756294045 chr2 243199373 3405382 0.014002429192118025 0.15870170535820288 chr3 198022430 2657900 0.013422216867048848 0.12551653495374765 chr4 191154276 2543206 0.013304468271481408 0.1367217459455017 chr5 180915260 2463160 0.013614993008328871 0.1258608319861689 chr6 171115067 1754799 0.01025508174566533 0.10901680926113168 chr7 159138663 2292604 0.014406329403433532 0.15010066081913223 chr8 146364022 2440973 0.016677411338149754 0.14226058234134464 chr9 141213431 1730444 0.012254103506627496 0.12546515493346017 chr10 135534747 2107750 0.015551362633229397 0.19247173059049827 chr11 135006516 1709970 0.012665833106899818 0.13704353321383658 chr12 133851895 1934121 0.014449709509155624 0.12917894287439918 chr13 115169878 701699 0.006092730253651914 0.08347099706695332 chr14 107349540 1262919 0.011764549713021592 0.11705705065152619 chr15 102531392 789662 0.0077016607752677345 0.09419687807816854 chr16 90354753 1149419 0.012721179150365228 0.12808921943662713 chr17 81195210 1692010 0.020838790859707117 0.16026108093738348 chr18 78077248 1068769 0.013688610028878067 0.14741015908079472 chr19 59128983 1163278 0.019673566852993228 0.17071662608813143 chr20 63025520 1059404 0.016809127477250486 0.14383070837311546 chr21 48129895 560047 0.01163615669637343 0.12308160068970207 chr22 51304566 440873 0.00859325074497268 0.09920454503608345 chrMT 16571 32180 1.941946774485547 2.06795769270171 chrX 155270560 1226205 0.007897215029043496 0.0982867900119172 chrY 59373566 139140 0.0023434671247470635 0.08428667234901795