BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524807.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 = 1,695,450 number of mapped reads = 1,555,807 (91.76%) number of supplementary alignments = 6,484 (0.38%) number of secondary alignments = 0 number of mapped bases = 89,250,407 bp number of sequenced bases = 89,221,959 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,677 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5442 >>>>>>> ACTG content number of A's = 20,699,156 bp (23.2%) number of C's = 18,099,792 bp (20.29%) number of T's = 28,829,429 bp (32.31%) number of G's = 21,582,710 bp (24.19%) number of N's = 10,872 bp (0.01%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 450,370 number of insertions = 6,418 mapped reads with insertion percentage = 0.41% number of deletions = 17,839 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.44% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.25X There is a 2.56% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 7125835 0.028589036093113685 0.3217795284560375 chr2 243199373 7487009 0.03078547821749524 0.39759973945464927 chr3 198022430 5810713 0.02934371121493661 0.19262088395638097 chr4 191154276 5702937 0.029834210980454343 0.21920277323579326 chr5 180915260 5349976 0.02957172324766855 0.18963151542671805 chr6 171115067 5085523 0.029719901871645235 0.2050049005354719 chr7 159138663 4924291 0.030943398085479704 0.3025450928413486 chr8 146364022 4435216 0.03030263817155831 0.23381638078392517 chr9 141213431 3821811 0.027064075796019715 0.21966139009337313 chr10 135534747 4344035 0.032051079860723836 0.29885236930547854 chr11 135006516 4063609 0.030099354611891473 0.2262129462581563 chr12 133851895 4003077 0.029906763740625415 0.19260588006779097 chr13 115169878 2718121 0.023600971427615823 0.16892038114607644 chr14 107349540 2685283 0.02501438757911771 0.1793628716106411 chr15 102531392 2603201 0.025389307110938276 0.17755019158082722 chr16 90354753 2708870 0.02998038188428228 0.2130273566093119 chr17 81195210 2554043 0.03145558709682505 0.20450821540879166 chr18 78077248 2292452 0.029361331997767134 0.35231052728861056 chr19 59128983 1995307 0.03374499101396687 0.27476969602077955 chr20 63025520 1926695 0.03057007701007465 0.20144928593098374 chr21 48129895 1180165 0.024520415014410483 0.1907365321223594 chr22 51304566 1160645 0.022622645321665913 0.16795870893443637 chrMT 16571 42073 2.5389535936274212 2.293131892382109 chrX 155270560 4930657 0.03175525997974117 0.2102529550087753 chrY 59373566 298863 0.005033603674739698 0.14216451583073778