BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716873.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,037,659 number of mapped reads = 911,097 (87.8%) number of supplementary alignments = 1,839 (0.18%) number of secondary alignments = 0 number of mapped bases = 51,991,430 bp number of sequenced bases = 51,975,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,909 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1291 >>>>>>> ACTG content number of A's = 12,884,498 bp (24.79%) number of C's = 8,578,713 bp (16.51%) number of T's = 17,015,480 bp (32.74%) number of G's = 13,496,234 bp (25.97%) number of N's = 566 bp (0%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 260,025 number of insertions = 3,582 mapped reads with insertion percentage = 0.39% number of deletions = 10,130 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.169X There is a 1.56% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 6127356 0.024583112272366214 0.23083634306397266 chr2 243199373 5336284 0.02194201380609645 0.2484559449173502 chr3 198022430 3334429 0.016838642975949746 0.13886727996508158 chr4 191154276 2228661 0.01165896492945834 0.1178593547536649 chr5 180915260 3793355 0.020967578964870073 0.1529837999398679 chr6 171115067 2009578 0.011744015505075306 0.13065487983177115 chr7 159138663 2745660 0.01725325542040026 0.2069596397076199 chr8 146364022 2190533 0.01496633510112205 0.14638721030142682 chr9 141213431 1441843 0.01021038147568272 0.1317774357740998 chr10 135534747 2400595 0.017712026274708727 0.19115791579563973 chr11 135006516 2605687 0.019300453616623955 0.17276632601463246 chr12 133851895 2095333 0.015654115319024806 0.13228550090461663 chr13 115169878 1564161 0.013581337648026336 0.12376467796442363 chr14 107349540 1129285 0.010519700410453551 0.11272003827058191 chr15 102531392 2268905 0.022128881269845628 0.15830393704488718 chr16 90354753 1572523 0.01740387691613744 0.14990155799273702 chr17 81195210 1958479 0.024120622386468366 0.1714685952205334 chr18 78077248 1688623 0.02162759373895965 0.24595915543905064 chr19 59128983 826940 0.013985358077273205 0.17664105171739736 chr20 63025520 1353487 0.02147522146584431 0.15527027246081485 chr21 48129895 655667 0.013622863710797625 0.12482530750804752 chr22 51304566 590347 0.011506714626530513 0.11304802253652363 chrMT 16571 500 0.03017319413433106 0.1710636504055231 chrX 155270560 1960082 0.01262365512174362 0.13724200323745403 chrY 59373566 113117 0.0019051744340233834 0.055808115882961924