BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238620.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 = 2,192,433 number of mapped reads = 1,981,106 (90.36%) number of supplementary alignments = 17,346 (0.79%) number of secondary alignments = 0 number of mapped bases = 122,373,679 bp number of sequenced bases = 122,317,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 469,160 duplication rate = 18.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.867 >>>>>>> ACTG content number of A's = 30,346,844 bp (24.81%) number of C's = 21,552,325 bp (17.62%) number of T's = 41,007,390 bp (33.53%) number of G's = 29,405,055 bp (24.04%) number of N's = 6,075 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 689,589 number of insertions = 7,589 mapped reads with insertion percentage = 0.38% number of deletions = 33,344 mapped reads with deletion percentage = 1.67% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.0395X std coverageData = 0.5783X There is a 2.17% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 5559446 0.022304642522836482 0.2630990031715996 chr2 243199373 3231232 0.013286350043344889 1.3978080947577287 chr3 198022430 10457881 0.05281159816087501 0.39050587786080976 chr4 191154276 4602638 0.02407813257601415 0.25487665263090337 chr5 180915260 10733983 0.059331551136150705 0.412115671013315 chr6 171115067 9782255 0.05716770107684322 0.6432106601510148 chr7 159138663 3215053 0.020202840336794838 0.42698344109268616 chr8 146364022 11298151 0.07719213264035611 0.608696139162388 chr9 141213431 6211769 0.043988514095376664 0.41727685104357076 chr10 135534747 15312455 0.11297807638951803 0.6157760896056319 chr11 135006516 6731379 0.049859660107072164 0.4083691784429953 chr12 133851895 2342361 0.01749964765160777 0.23176015783826112 chr13 115169878 7684043 0.06671920760391879 0.514839031644473 chr14 107349540 1611508 0.015011783003448362 0.2203263633171061 chr15 102531392 2577305 0.025136740560393445 0.36753523387681536 chr16 90354753 3000960 0.03321308398684904 0.33549166092695804 chr17 81195210 491190 0.006049494791626255 0.12957200312743455 chr18 78077248 10212744 0.13080307338701283 1.2349982574240457 chr19 59128983 441128 0.007460436111339849 0.268282251349635 chr20 63025520 1397781 0.022178016143301952 0.25276626868098817 chr21 48129895 2153962 0.04475309991846024 0.36632775498767617 chr22 51304566 1016426 0.01981160897063236 0.22863888218534542 chrMT 16571 6429 0.3879669301792288 0.7694000005341106 chrX 155270560 2096680 0.013503396909240233 0.20797286530378933 chrY 59373566 204920 0.0034513675665025748 0.20924166148377168