BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524302.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 = 656,563 number of mapped reads = 578,860 (88.17%) number of supplementary alignments = 4,847 (0.74%) number of secondary alignments = 0 number of mapped bases = 33,082,842 bp number of sequenced bases = 33,075,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,957 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7634 >>>>>>> ACTG content number of A's = 7,701,100 bp (23.28%) number of C's = 6,244,988 bp (18.88%) number of T's = 10,570,944 bp (31.96%) number of G's = 8,553,287 bp (25.86%) number of N's = 4,682 bp (0.01%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 168,778 number of insertions = 2,267 mapped reads with insertion percentage = 0.39% number of deletions = 4,808 mapped reads with deletion percentage = 0.83% homopolymer indels = 40.48% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1499X There is a 1.01% of reference with a coverageData >= 1X There is a 0.03% 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 2838731 0.011389062898262548 0.28450577467857663 chr2 243199373 2189037 0.009000997712276174 0.1619212692859195 chr3 198022430 2280765 0.011517710392706524 0.11133142084055908 chr4 191154276 1728372 0.009041764778518478 0.10237091073388241 chr5 180915260 1917774 0.010600399325076282 0.10653731493740101 chr6 171115067 2070298 0.012098864444239734 0.11762458222495088 chr7 159138663 1565553 0.009837665910263428 0.18348281347048254 chr8 146364022 3227266 0.022049585382396774 0.17802462919088083 chr9 141213431 1373913 0.009729336581305783 0.12089963114126384 chr10 135534747 1699972 0.012542702425969039 0.1632291030744266 chr11 135006516 1563306 0.011579485541275652 0.12820130562856547 chr12 133851895 1337815 0.009994740829033462 0.10377020734274256 chr13 115169878 818928 0.007110609251491957 0.08657013705228485 chr14 107349540 711251 0.006625561693138136 0.09033990415963865 chr15 102531392 1011184 0.009862189328318102 0.10469001091440576 chr16 90354753 1074688 0.011894094824209193 0.12101803265058182 chr17 81195210 1038474 0.012789843144687969 0.12241255850048445 chr18 78077248 767975 0.009836092071277922 0.19302075843566943 chr19 59128983 669546 0.01132348242823659 0.20276917230089248 chr20 63025520 732425 0.011621086188578848 0.11171126495082619 chr21 48129895 459856 0.009554477523792645 0.1048845622505765 chr22 51304566 261638 0.005099702042114536 0.07310838363790363 chrMT 16571 13573 0.819081527970551 1.023770321378746 chrX 155270560 1622578 0.01045000417336036 0.11825577310127025 chrY 59373566 107924 0.0018177112690182697 0.06098342040135005