BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716821.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 = 790,606 number of mapped reads = 659,625 (83.43%) number of supplementary alignments = 3,038 (0.38%) number of secondary alignments = 0 number of mapped bases = 38,345,114 bp number of sequenced bases = 38,333,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,903 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6512 >>>>>>> ACTG content number of A's = 9,222,719 bp (24.06%) number of C's = 6,937,012 bp (18.1%) number of T's = 12,514,259 bp (32.65%) number of G's = 9,659,095 bp (25.2%) number of N's = 232 bp (0%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 197,085 number of insertions = 2,549 mapped reads with insertion percentage = 0.38% number of deletions = 7,450 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 0.1437X There is a 1.17% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0% 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 4501824 0.018061435441719523 0.2216208495836764 chr2 243199373 3930085 0.016159930642584346 0.19010360028138307 chr3 198022430 2449263 0.0123686139999393 0.11552570159478068 chr4 191154276 1620005 0.008474856194166434 0.10042829991810924 chr5 180915260 2755115 0.015228759586117833 0.12833181424883558 chr6 171115067 1440726 0.008419632620662212 0.10039123129729459 chr7 159138663 2577592 0.016197145001777474 0.20627919682647353 chr8 146364022 1704505 0.011645655651632749 0.12926696467394636 chr9 141213431 1052553 0.007453632367306478 0.10856264960451671 chr10 135534747 1720219 0.012692088472338388 0.133295516356576 chr11 135006516 1636367 0.012120652013566515 0.1353455019817758 chr12 133851895 1523946 0.01138531509023462 0.11121475360738198 chr13 115169878 1123455 0.009754764175403573 0.10230521199544633 chr14 107349540 824853 0.007683805631584448 0.09327655402603224 chr15 102531392 1660057 0.016190719423764384 0.13304385971547392 chr16 90354753 1137036 0.012584130466274419 0.11937475258589733 chr17 81195210 1429596 0.017606900702639972 0.1427195458564765 chr18 78077248 1243436 0.01592571500470918 0.22182458605139974 chr19 59128983 593665 0.010040169302421454 0.15677251080161614 chr20 63025520 987577 0.015669478014620108 0.13115130438875536 chr21 48129895 475708 0.009883836231099195 0.10514540883362027 chr22 51304566 435377 0.008486125776797332 0.09514011199181145 chrMT 16571 807 0.04869953533281033 0.2152391474411165 chrX 155270560 1426891 0.009189707308326833 0.10723902320212547 chrY 59373566 94456 0.0015908763169118056 0.048347382134374166