BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124803.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 485,728 number of mapped reads = 478,596 (98.53%) number of supplementary alignments = 152,389 (31.37%) number of secondary alignments = 0 number of mapped bases = 69,817,256 bp number of sequenced bases = 69,767,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 542,729 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.5413 >>>>>>> ACTG content number of A's = 20,337,011 bp (29.15%) number of C's = 11,453,471 bp (16.42%) number of T's = 21,695,878 bp (31.1%) number of G's = 16,280,698 bp (23.34%) number of N's = 0 bp (0%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 839,568 number of insertions = 17,497 mapped reads with insertion percentage = 3.6% number of deletions = 41,390 mapped reads with deletion percentage = 8.42% homopolymer indels = 83.5% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 45.6007X There is a 0.33% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 12997777 0.05214742072799088 45.42159705597385 chr2 243199373 980135 0.004030170752126075 0.12440115096486414 chr3 198022430 684944 0.0034589212949260343 0.06582693262383997 chr4 191154276 685987 0.003588656316534609 0.07197174370891926 chr5 180915260 630632 0.0034857866605614144 0.06260634573884984 chr6 171115067 602013 0.003518176456080282 0.06228189748183937 chr7 159138663 774855 0.004869055610954832 0.07745450303492019 chr8 146364022 43148842 0.2948049760480072 200.31834978729154 chr9 141213431 427460 0.0030270491763634013 0.06889512318511866 chr10 135534747 4550500 0.033574416160602714 19.14641106962774 chr11 135006516 525651 0.003893523183725443 0.06724851242151732 chr12 133851895 498975 0.0037278142382668545 0.10817930034137661 chr13 115169878 437278 0.003796808745425605 0.46417306846166545 chr14 107349540 315036 0.0029346748947410486 0.06496055399405057 chr15 102531392 429410 0.0041880831969978525 0.8850120345555756 chr16 90354753 373168 0.004130031764903392 0.10319852990404527 chr17 81195210 274063 0.003375359211460873 0.06487000794011834 chr18 78077248 284301 0.0036412784426008457 0.08002055794243336 chr19 59128983 169268 0.0028626908736110006 0.06217169532507639 chr20 63025520 231622 0.0036750509952159062 0.07662070689244564 chr21 48129895 149521 0.003106613883117759 0.06516896548112727 chr22 51304566 115569 0.0022526065223902295 0.04974200899659462 chrMT 16571 3290 0.1985396174038984 0.4382172767350803 chrX 155270560 328371 0.0021148310407330274 0.048529768794645774 chrY 59373566 198588 0.003344720780287982 0.11409584794097581