BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237273.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 = 1,644,677 number of mapped reads = 1,417,883 (86.21%) number of supplementary alignments = 12,997 (0.79%) number of secondary alignments = 0 number of mapped bases = 93,556,464 bp number of sequenced bases = 93,502,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,776 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0689 >>>>>>> ACTG content number of A's = 26,790,686 bp (28.65%) number of C's = 16,439,927 bp (17.58%) number of T's = 30,539,206 bp (32.66%) number of G's = 19,731,559 bp (21.1%) number of N's = 1,323 bp (0%) GC percentage = 38.68% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 766,105 number of insertions = 7,441 mapped reads with insertion percentage = 0.52% number of deletions = 30,756 mapped reads with deletion percentage = 2.14% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.3377X There is a 2.35% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.11% 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 9071443 0.036394866193733576 0.5728850532600427 chr2 243199373 7489429 0.030795428901044083 0.3475551450055972 chr3 198022430 5941798 0.03000568167959559 0.21394059620422484 chr4 191154276 4077497 0.02133092225465048 0.21834340011768075 chr5 180915260 4882413 0.02698729228258578 0.2027006373738379 chr6 171115067 10794111 0.06308100852393086 0.4151679936792945 chr7 159138663 5965473 0.03748600677888063 0.43077252527994203 chr8 146364022 6227691 0.042549329506673436 0.5766101855615078 chr9 141213431 4434084 0.031399874421293536 0.32361714767099586 chr10 135534747 3146751 0.023217300874144104 0.32510384720054314 chr11 135006516 3419179 0.025326029448830455 0.2411382520356394 chr12 133851895 2383088 0.017803916784293567 0.16853042851327799 chr13 115169878 2961904 0.025717696774845936 0.19667109977334957 chr14 107349540 2623026 0.024434440985960443 0.20829808923733356 chr15 102531392 2534799 0.024722174843778578 0.193073060163611 chr16 90354753 1546521 0.01711610013476546 0.1908297219673852 chr17 81195210 1694574 0.020870369077190636 0.21100991274318137 chr18 78077248 2202842 0.028213622488333607 0.5219398690282652 chr19 59128983 1781913 0.030136033288446717 0.35750961235076756 chr20 63025520 1474475 0.0233948882928693 0.1915824208974344 chr21 48129895 1845159 0.03833706680639964 0.26892586467688895 chr22 51304566 991378 0.019323387318002067 0.1665693922965184 chrMT 16571 36458 2.200108623498884 1.948557580028148 chrX 155270560 5748115 0.03701999271465241 0.2540728234705976 chrY 59373566 282343 0.004755365375898089 0.15716081346772337