BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524634.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 = 1,148,658 number of mapped reads = 1,074,502 (93.54%) number of supplementary alignments = 2,398 (0.21%) number of secondary alignments = 0 number of mapped bases = 62,935,964 bp number of sequenced bases = 62,915,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,028 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4792 >>>>>>> ACTG content number of A's = 16,152,973 bp (25.67%) number of C's = 11,725,865 bp (18.64%) number of T's = 19,137,946 bp (30.42%) number of G's = 15,898,727 bp (25.27%) number of N's = 332 bp (0%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 285,442 number of insertions = 4,337 mapped reads with insertion percentage = 0.4% number of deletions = 11,714 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.1918X There is a 1.85% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6290140 0.025236205931057642 0.29934002461687087 chr2 243199373 5575084 0.02292392423232111 0.22082033284909677 chr3 198022430 3917525 0.019783238696747637 0.15154101634962894 chr4 191154276 2733662 0.014300815326778252 0.14250643755076023 chr5 180915260 3823842 0.021136094323939286 0.15608089033480027 chr6 171115067 4033527 0.023572015432165305 0.17173558292374796 chr7 159138663 3748134 0.0235526296962794 0.24662015657287037 chr8 146364022 5356869 0.036599629654888825 0.2564669695822664 chr9 141213431 2300465 0.016290695465079382 0.173909274960827 chr10 135534747 2630484 0.019408189104451568 0.1926520164790233 chr11 135006516 3945311 0.029223115423554817 0.20553076946586388 chr12 133851895 2071958 0.01547948200509227 0.1363023769398061 chr13 115169878 1413393 0.012272245352209195 0.11910391802845646 chr14 107349540 1130252 0.010528708367078239 0.11484171786987397 chr15 102531392 1640818 0.016003079330084585 0.1392801446677095 chr16 90354753 1963170 0.02172735727582588 0.1638124542868465 chr17 81195210 1499507 0.01846792440095912 0.14882703979388717 chr18 78077248 1616361 0.020702074437869533 0.24897053391396273 chr19 59128983 1299639 0.021979728621410587 0.21932557071427627 chr20 63025520 1196082 0.018977741080121194 0.15009790155098565 chr21 48129895 553669 0.011503640305053646 0.12479986184305668 chr22 51304566 1274897 0.02484958161423683 0.16971125787932342 chrMT 16571 51770 3.124132520668638 2.5100323178712083 chrX 155270560 2722816 0.01753594499820185 0.15435296094579537 chrY 59373566 146589 0.0024689269969063337 0.08060663199110552