BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231767.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 = 1,046,265 number of mapped reads = 721,066 (68.92%) number of supplementary alignments = 3,787 (0.36%) number of secondary alignments = 0 number of mapped bases = 46,394,182 bp number of sequenced bases = 46,366,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,543 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8692 >>>>>>> ACTG content number of A's = 13,082,473 bp (28.22%) number of C's = 7,840,858 bp (16.91%) number of T's = 15,063,778 bp (32.49%) number of G's = 10,377,145 bp (22.38%) number of N's = 2,093 bp (0%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 435,375 number of insertions = 3,816 mapped reads with insertion percentage = 0.53% number of deletions = 15,963 mapped reads with deletion percentage = 2.19% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1666X There is a 1.39% of reference with a coverageData >= 1X There is a 0.09% 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 4408075 0.017685312005702083 0.2484373049376436 chr2 243199373 2445378 0.01005503414681912 0.16218243513582847 chr3 198022430 4990171 0.025200029107813694 0.1688929104328363 chr4 191154276 1784323 0.009334465528775301 0.10441266983818022 chr5 180915260 2678612 0.014805893101554838 0.12947540178289269 chr6 171115067 3219015 0.018811990413445008 0.15942366149850193 chr7 159138663 2200665 0.013828600533108663 0.16005075133461072 chr8 146364022 3008593 0.020555550188419938 0.32192244858034896 chr9 141213431 1939424 0.013733991067747656 0.13913783963837575 chr10 135534747 2019814 0.014902554840789277 0.1491911704460921 chr11 135006516 2127734 0.01576023189873295 0.1455491270751923 chr12 133851895 1459683 0.01090520982164653 0.11058961589418245 chr13 115169878 2231093 0.01937219209349167 0.14850847226164737 chr14 107349540 2157684 0.020099611046307232 0.15457261072246894 chr15 102531392 769809 0.007508032271716354 0.09250036190668026 chr16 90354753 1240633 0.01373068885485194 0.1281548053216706 chr17 81195210 1019593 0.012557304796674582 0.12239109906413924 chr18 78077248 1018397 0.013043454093054099 0.20635533197837203 chr19 59128983 1180516 0.019965099010750786 0.18913561479150967 chr20 63025520 1069050 0.016962176591323642 0.1410431884201281 chr21 48129895 806898 0.01676500644765587 0.14002901361280048 chr22 51304566 360971 0.007035845503497681 0.08774362957186124 chrMT 16571 6545 0.39496711121839356 0.7827696134804508 chrX 155270560 2144707 0.013812708603614233 0.1283607822265865 chrY 59373566 106799 0.0017987634429773008 0.04936100696524221