BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231808.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 = 4,120,015 number of mapped reads = 3,775,583 (91.64%) number of supplementary alignments = 29,042 (0.7%) number of secondary alignments = 0 number of mapped bases = 239,599,449 bp number of sequenced bases = 239,509,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 615,304 duplication rate = 13.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9981 >>>>>>> ACTG content number of A's = 61,276,029 bp (25.58%) number of C's = 42,302,861 bp (17.66%) number of T's = 79,272,943 bp (33.1%) number of G's = 56,568,015 bp (23.62%) number of N's = 89,833 bp (0.04%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,535,884 number of insertions = 15,885 mapped reads with insertion percentage = 0.42% number of deletions = 51,137 mapped reads with deletion percentage = 1.34% homopolymer indels = 44.09% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.9278X There is a 5.11% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 19495211 0.07821529560000574 1.8808675391482017 chr2 243199373 20286667 0.08341578660237746 1.8078475288302844 chr3 198022430 18807596 0.09497709931142649 0.43820476638420097 chr4 191154276 7899652 0.041326054354128075 0.316122654842787 chr5 180915260 13237651 0.07317045007701396 0.39566623163218634 chr6 171115067 20764823 0.12135005621684969 0.8862779711012644 chr7 159138663 15858728 0.09965352040189002 0.9970096657905714 chr8 146364022 12345611 0.08434867279063976 0.7896472702990205 chr9 141213431 7065939 0.05003730133856744 0.5896670624504863 chr10 135534747 12626911 0.09316364459661404 0.6155328727378048 chr11 135006516 7380402 0.0546670058502954 0.4778113429221517 chr12 133851895 7135095 0.05330589454859791 0.3427357765088868 chr13 115169878 6038402 0.052430393301276225 0.3918923990342283 chr14 107349540 9090602 0.08468226319367554 0.42681911294046837 chr15 102531392 6138794 0.05987233646452396 0.40884940086523835 chr16 90354753 7244295 0.08017613638985877 0.43491956057687386 chr17 81195210 8467056 0.10428024017672964 0.5262769582054392 chr18 78077248 7670228 0.09823896457006272 1.3356131066568238 chr19 59128983 8820676 0.14917685967979527 1.13638174214578 chr20 63025520 7424829 0.1178067075051503 0.5007015846629825 chr21 48129895 6498764 0.1350255179239431 0.5480411069580858 chr22 51304566 2444373 0.047644355864934124 0.30055407284026653 chrMT 16571 157729 9.518375475227808 6.361251694784477 chrX 155270560 6130918 0.0394853860255286 0.3544581370334835 chrY 59373566 568497 0.009574917565166964 0.24774344374402324