BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063602.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 = 7,844,283 number of mapped reads = 6,902,961 (88%) number of supplementary alignments = 58,239 (0.74%) number of secondary alignments = 0 number of mapped bases = 443,592,492 bp number of sequenced bases = 443,419,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,085,357 duplication rate = 12.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0557 >>>>>>> ACTG content number of A's = 116,161,938 bp (26.2%) number of C's = 79,520,883 bp (17.93%) number of T's = 144,288,645 bp (32.54%) number of G's = 103,396,409 bp (23.32%) number of N's = 51,493 bp (0.01%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 2,419,190 number of insertions = 29,340 mapped reads with insertion percentage = 0.42% number of deletions = 98,519 mapped reads with deletion percentage = 1.41% homopolymer indels = 44.92% >>>>>>> Coverage mean coverageData = 0.1433X std coverageData = 1.4997X There is a 9.47% of reference with a coverageData >= 1X There is a 2.93% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 41917835 0.16817544859797962 3.731736134718464 chr2 243199373 42155366 0.1733366557651446 2.0454824629266035 chr3 198022430 23056485 0.11643370400009737 0.48757841262978785 chr4 191154276 25235948 0.13201874699365868 0.5973805270621346 chr5 180915260 22372104 0.12366067959109696 0.5074617300523107 chr6 171115067 27127151 0.15853163298589013 0.8680837854259308 chr7 159138663 24768940 0.15564376081254372 1.5402733921638005 chr8 146364022 22505126 0.1537613253071168 1.413308432156054 chr9 141213431 17173022 0.12161040120893317 0.9697489107699926 chr10 135534747 21688860 0.16002435154138 1.0637909378451778 chr11 135006516 18611688 0.13785770162382385 1.0297412546618328 chr12 133851895 22678839 0.16943233414812692 0.6146804966544814 chr13 115169878 13042750 0.11324792755272346 0.5297078631657399 chr14 107349540 11778001 0.10971636208222224 0.5565019699970313 chr15 102531392 9987668 0.09741083004120338 0.4991448865801243 chr16 90354753 13608037 0.1506067644277662 0.6524569790235668 chr17 81195210 12241115 0.15076154122884836 0.6909326690610117 chr18 78077248 12531804 0.16050519608478003 2.1587494340590436 chr19 59128983 8498210 0.14372325666416416 2.3140602991138715 chr20 63025520 7796022 0.12369627414418795 0.5677550569271487 chr21 48129895 9825844 0.20415261658060962 0.7078593282719985 chr22 51304566 5378399 0.10483275504172475 0.44622122762118505 chrMT 16571 606181 36.580833987085875 19.44203274655702 chrX 155270560 27772855 0.17886748782254666 0.7190524992350747 chrY 59373566 1234242 0.02078773574085141 0.556564312866987