BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264629.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,377,589,288 number of mapped reads = 1,369,699,258 (99.43%) number of supplementary alignments = 9,717,583 (0.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 686,625,899 number of mapped paired reads (second in pair) = 683,073,359 number of mapped paired reads (both in pair) = 1,364,871,998 number of mapped paired reads (singletons) = 4,827,260 number of mapped bases = 137,440,396,842 bp number of sequenced bases = 137,408,873,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 570,371,279 duplication rate = 41.51% >>>>>>> Insert size mean insert size = 89,988.832 std insert size = 2,886,188.5301 median insert size = 300 >>>>>>> Mapping quality mean mapping quality = 54.4458 >>>>>>> ACTG content number of A's = 42,558,316,055 bp (30.97%) number of C's = 26,126,222,806 bp (19.01%) number of T's = 42,304,350,603 bp (30.79%) number of G's = 26,381,959,299 bp (19.2%) number of N's = 38,025,119 bp (0.03%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 525,198,015 number of insertions = 15,160,086 mapped reads with insertion percentage = 1.09% number of deletions = 14,158,626 mapped reads with deletion percentage = 1.01% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 44.3973X std coverageData = 45.4889X There is a 90.5% of reference with a coverageData >= 1X There is a 89.12% of reference with a coverageData >= 2X There is a 87.74% of reference with a coverageData >= 3X There is a 86.38% of reference with a coverageData >= 4X There is a 85.01% of reference with a coverageData >= 5X There is a 83.65% of reference with a coverageData >= 6X There is a 82.29% of reference with a coverageData >= 7X There is a 80.94% of reference with a coverageData >= 8X There is a 79.59% of reference with a coverageData >= 9X There is a 78.24% of reference with a coverageData >= 10X There is a 76.91% of reference with a coverageData >= 11X There is a 75.58% of reference with a coverageData >= 12X There is a 74.26% of reference with a coverageData >= 13X There is a 72.95% of reference with a coverageData >= 14X There is a 71.64% of reference with a coverageData >= 15X There is a 70.35% of reference with a coverageData >= 16X There is a 69.06% of reference with a coverageData >= 17X There is a 67.79% of reference with a coverageData >= 18X There is a 66.52% of reference with a coverageData >= 19X There is a 65.27% of reference with a coverageData >= 20X There is a 64.03% of reference with a coverageData >= 21X There is a 62.8% of reference with a coverageData >= 22X There is a 61.59% of reference with a coverageData >= 23X There is a 60.38% of reference with a coverageData >= 24X There is a 59.19% of reference with a coverageData >= 25X There is a 58.02% of reference with a coverageData >= 26X There is a 56.85% of reference with a coverageData >= 27X There is a 55.7% of reference with a coverageData >= 28X There is a 54.57% of reference with a coverageData >= 29X There is a 53.45% of reference with a coverageData >= 30X There is a 52.35% of reference with a coverageData >= 31X There is a 51.26% of reference with a coverageData >= 32X There is a 50.19% of reference with a coverageData >= 33X There is a 49.13% of reference with a coverageData >= 34X There is a 48.09% of reference with a coverageData >= 35X There is a 47.06% of reference with a coverageData >= 36X There is a 46.05% of reference with a coverageData >= 37X There is a 45.06% of reference with a coverageData >= 38X There is a 44.09% of reference with a coverageData >= 39X There is a 43.13% of reference with a coverageData >= 40X There is a 42.19% of reference with a coverageData >= 41X There is a 41.26% of reference with a coverageData >= 42X There is a 40.35% of reference with a coverageData >= 43X There is a 39.45% of reference with a coverageData >= 44X There is a 38.58% of reference with a coverageData >= 45X There is a 37.71% of reference with a coverageData >= 46X There is a 36.87% of reference with a coverageData >= 47X There is a 36.04% of reference with a coverageData >= 48X There is a 35.22% of reference with a coverageData >= 49X There is a 34.42% of reference with a coverageData >= 50X There is a 33.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10423511352 41.81939972779446 45.90121403133958 chr2 243199373 12500967332 51.40213635336963 46.50617362677801 chr3 198022430 11573013066 58.442940357817044 49.108238126552145 chr4 191154276 11037132180 57.73939464477373 46.45991649878461 chr5 180915260 9486749083 52.43752839312726 44.77444899332527 chr6 171115067 9912727214 57.93018340109115 50.25074907487143 chr7 159138663 7715116776 48.48046747759845 46.661201661030326 chr8 146364022 7445266760 50.86814818466795 43.70547600206589 chr9 141213431 5679854251 40.221770767682855 47.41724912650169 chr10 135534747 5873007181 43.33211453886434 41.203368960856984 chr11 135006516 6421110353 47.56148475826159 46.37631505802076 chr12 133851895 6319209544 47.21046006857056 47.85477521003139 chr13 115169878 5325599301 46.241251562322574 45.867228406314545 chr14 107349540 4278557472 39.85631863909244 43.48124658562748 chr15 102531392 3644243963 35.542714206006295 43.50106678410931 chr16 90354753 2511876848 27.80016285363538 35.121809354619465 chr17 81195210 2278718877 28.064695897701355 34.92074985231816 chr18 78077248 4045645407 51.81593243399153 45.08963426876135 chr19 59128983 1090587617 18.4442140159928 26.85041674616123 chr20 63025520 2208360161 35.03914225539115 43.788263911537285 chr21 48129895 1752642593 36.41484347721931 46.96564827147847 chr22 51304566 719346152 14.021094184872355 24.841431145926148 chrMT 16571 33767 2.0377164926679137 5.148644010108602 chrX 155270560 4557082282 29.349300227937608 31.193762152960474 chrY 59373566 640037310 10.779836097430968 24.38927426811562