BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,576,150 number of mapped reads = 3,471,860 (97.08%) number of supplementary alignments = 32,045 (0.9%) number of secondary alignments = 0 number of mapped bases = 269,789,515 bp number of sequenced bases = 269,621,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 703,101 duplication rate = 18.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2343 >>>>>>> ACTG content number of A's = 79,062,998 bp (29.32%) number of C's = 53,736,640 bp (19.93%) number of T's = 79,957,000 bp (29.66%) number of G's = 56,843,453 bp (21.08%) number of N's = 21,134 bp (0.01%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,518,379 number of insertions = 33,435 mapped reads with insertion percentage = 0.95% number of deletions = 93,962 mapped reads with deletion percentage = 2.66% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.0871X std coverageData = 0.7924X There is a 5.99% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 22543246 0.09044409161171157 1.5284068913706315 chr2 243199373 23788526 0.09781491500802512 1.1374602221304446 chr3 198022430 18678077 0.0943230370418139 0.41946980381118876 chr4 191154276 17065716 0.08927718676824159 0.45861804969551767 chr5 180915260 16432580 0.0908302594264298 0.42582225920193584 chr6 171115067 15753358 0.09206295083296201 0.49021237852100985 chr7 159138663 14562925 0.09151091711760831 1.0629425452005816 chr8 146364022 13078394 0.08935525152485903 0.5626301395200034 chr9 141213431 11782091 0.08343463448600721 0.7945644310715586 chr10 135534747 16107710 0.11884561233585363 0.8470469416986265 chr11 135006516 12351753 0.09149005074688395 0.5236593012647737 chr12 133851895 12109550 0.09046976884413926 0.4162368313607354 chr13 115169878 7964776 0.0691567633682828 0.3538584665114912 chr14 107349540 7820482 0.07285063354719545 0.4973023508348819 chr15 102531392 7916521 0.07721070440553465 0.3760789890867611 chr16 90354753 7383523 0.08171704038635355 0.6920730683829707 chr17 81195210 7488296 0.0922258345042768 0.4893988828592029 chr18 78077248 6369145 0.08157491667739108 0.919768608964328 chr19 59128983 5378174 0.09095664642160343 1.5182882479007975 chr20 63025520 5498916 0.08724903816739632 0.4375163222750391 chr21 48129895 3199849 0.06648360649862212 0.38105429229065374 chr22 51304566 3150813 0.06141389052974349 0.3614184866563389 chrMT 16571 325408 19.637197513728804 10.469929222407051 chrX 155270560 12345706 0.0795109259604654 0.44272013976715574 chrY 59373566 693980 0.01168836650303268 0.8149190435483143