BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004026.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 = 2,075,163 number of mapped reads = 1,751,310 (84.39%) number of supplementary alignments = 22,604 (1.09%) number of secondary alignments = 0 number of mapped bases = 115,185,861 bp number of sequenced bases = 115,122,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,051 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5337 >>>>>>> ACTG content number of A's = 31,822,061 bp (27.64%) number of C's = 21,535,660 bp (18.71%) number of T's = 36,171,533 bp (31.42%) number of G's = 25,573,900 bp (22.21%) number of N's = 19,178 bp (0.02%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,122,228 number of insertions = 9,088 mapped reads with insertion percentage = 0.51% number of deletions = 37,649 mapped reads with deletion percentage = 2.12% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0372X std coverageData = 0.3433X There is a 2.99% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9489651 0.03807272761017514 0.5903033061039791 chr2 243199373 8605242 0.035383487604632925 0.363960636192191 chr3 198022430 4509925 0.022774818993989723 0.18050098242003076 chr4 191154276 10202408 0.053372638130260816 0.30043218513712067 chr5 180915260 5862742 0.03240601152163726 0.21705072129301556 chr6 171115067 6845869 0.04000740040033997 0.2819698561886135 chr7 159138663 4741405 0.029794173902290482 0.3162184366153994 chr8 146364022 8679177 0.059298568605883215 0.42403362676380624 chr9 141213431 7067518 0.050048482994510625 0.40428214885128194 chr10 135534747 5708211 0.042116218359857197 0.34557957251420374 chr11 135006516 5568802 0.041248394262688774 0.34381621642926935 chr12 133851895 4558788 0.0340584494526581 0.23056633929126094 chr13 115169878 2403958 0.020873148793298192 0.17494146078199144 chr14 107349540 2739349 0.025518032028828443 0.23624106342221354 chr15 102531392 3812922 0.03718784974654397 0.22905926002019172 chr16 90354753 3494609 0.038676537580707014 0.2643562504289847 chr17 81195210 3435504 0.042311658532566146 0.27847157542504514 chr18 78077248 2752001 0.0352471567645417 0.6433500434706175 chr19 59128983 1898008 0.03209945281825666 0.4556902245786387 chr20 63025520 2832039 0.04493479784062075 0.26387410304205156 chr21 48129895 2036572 0.04231407527483698 0.27621212944937884 chr22 51304566 1033858 0.020151383796911955 0.16674863319885064 chrMT 16571 29697 1.792106692414459 1.7656780742721927 chrX 155270560 6528748 0.04204755879028194 0.2737493621149197 chrY 59373566 348858 0.005875645064000367 0.1709805803790262