BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524776.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 = 1,934,455 number of mapped reads = 1,765,409 (91.26%) number of supplementary alignments = 6,316 (0.33%) number of secondary alignments = 0 number of mapped bases = 101,318,552 bp number of sequenced bases = 101,285,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,598 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5334 >>>>>>> ACTG content number of A's = 25,128,631 bp (24.81%) number of C's = 19,629,801 bp (19.38%) number of T's = 31,954,706 bp (31.55%) number of G's = 24,560,346 bp (24.25%) number of N's = 12,219 bp (0.01%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 513,549 number of insertions = 8,197 mapped reads with insertion percentage = 0.46% number of deletions = 20,324 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.2806X There is a 2.86% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8077224 0.032406033604225205 0.3700637165553715 chr2 243199373 8536864 0.035102327340292935 0.4848162654298963 chr3 198022430 6653500 0.0335997290811955 0.20884536145215307 chr4 191154276 6409282 0.033529367661124146 0.23334945260075332 chr5 180915260 5994809 0.033136005221450084 0.2044316904396728 chr6 171115067 5738607 0.03353653831079644 0.2290528842789944 chr7 159138663 5513388 0.03464518235898463 0.3292275977806102 chr8 146364022 5055405 0.03453994315624915 0.25692402187055746 chr9 141213431 4340292 0.03073568830715543 0.24098939413867523 chr10 135534747 4850870 0.035790600619928115 0.3140438096527127 chr11 135006516 4570817 0.03385626957442558 0.2520855523465019 chr12 133851895 4635991 0.03463522873546168 0.21484697365968733 chr13 115169878 3116364 0.027058846063898755 0.18570322914157056 chr14 107349540 3018743 0.028120688733272635 0.1918335720091059 chr15 102531392 2956313 0.028833247479952286 0.19367179334817994 chr16 90354753 3130938 0.034651613734144125 0.22921503776632374 chr17 81195210 2940807 0.036218971537853036 0.2242658118377481 chr18 78077248 2658806 0.034053531190033744 0.3650410879640026 chr19 59128983 2294242 0.038800633523495574 0.31464793810199876 chr20 63025520 2202019 0.03493852966227014 0.22042374783621915 chr21 48129895 1353970 0.02813158017485806 0.20803546174650187 chr22 51304566 1305745 0.025450853633573276 0.1816625813747356 chrMT 16571 44542 2.687948826262748 2.2599095222490377 chrX 155270560 5574179 0.035899780357590005 0.22959882818458682 chrY 59373566 344835 0.005807887638077861 0.16021331781314005