BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004079.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 = 3,026,184 number of mapped reads = 2,712,215 (89.62%) number of supplementary alignments = 22,824 (0.75%) number of secondary alignments = 0 number of mapped bases = 176,493,992 bp number of sequenced bases = 176,403,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,667 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0667 >>>>>>> ACTG content number of A's = 48,479,237 bp (27.48%) number of C's = 34,309,163 bp (19.45%) number of T's = 52,694,567 bp (29.87%) number of G's = 40,884,515 bp (23.18%) number of N's = 36,343 bp (0.02%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,530,222 number of insertions = 14,454 mapped reads with insertion percentage = 0.53% number of deletions = 53,708 mapped reads with deletion percentage = 1.95% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.057X std coverageData = 0.4837X There is a 4.9% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 13397715 0.05375198242735772 0.8299696061078486 chr2 243199373 14951175 0.061477029383624274 0.6099898891117271 chr3 198022430 9873956 0.04986281604563685 0.2511031953550888 chr4 191154276 11439517 0.059844421162726175 0.2910618570199968 chr5 180915260 8299631 0.045875792898841146 0.24712919448076692 chr6 171115067 10163490 0.059395646322599985 0.3421993657992634 chr7 159138663 12972651 0.08151790869325073 0.77227437347982 chr8 146364022 12554495 0.08577582679437437 0.6017593608192093 chr9 141213431 7137511 0.05054413698085135 0.4805817770626734 chr10 135534747 8450509 0.06234939148113804 0.4538891040659883 chr11 135006516 8795365 0.0651477073891752 0.447276982730544 chr12 133851895 7391273 0.05521978601797158 0.27506668700478204 chr13 115169878 6057370 0.05259508914301359 0.2544963006160417 chr14 107349540 4356555 0.040582893974207994 0.3026533364971264 chr15 102531392 6240301 0.060862345456111626 0.2952495255249698 chr16 90354753 4811817 0.05325471920663653 0.32469349411435916 chr17 81195210 4370195 0.053823310513021645 0.29064256639684394 chr18 78077248 4778734 0.06120520538838664 0.8716811241348738 chr19 59128983 3226242 0.054562785224971655 0.6304523235834876 chr20 63025520 4167719 0.06612748296245712 0.33563471309755794 chr21 48129895 1842165 0.03827486014669261 0.25819616753997193 chr22 51304566 1906562 0.03716164366345093 0.2132350591353954 chrMT 16571 9668 0.5834288817814254 0.916057521954444 chrX 155270560 8835671 0.05690499860372759 0.32778112809594157 chrY 59373566 463705 0.007809957043846752 0.15556229567256868