BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781825.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 146,096,708 number of mapped reads = 142,646,447 (97.64%) number of supplementary alignments = 485,832 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 71,935,496 number of mapped paired reads (second in pair) = 70,710,951 number of mapped paired reads (both in pair) = 140,321,610 number of mapped paired reads (singletons) = 2,324,837 number of mapped bases = 14,161,665,368 bp number of sequenced bases = 14,158,775,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,208,280 duplication rate = 5.53% >>>>>>> Insert size mean insert size = 41,832.2852 std insert size = 2,029,126.6346 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.9613 >>>>>>> ACTG content number of A's = 4,176,865,488 bp (29.5%) number of C's = 2,888,234,093 bp (20.4%) number of T's = 4,159,569,590 bp (29.38%) number of G's = 2,932,097,048 bp (20.71%) number of N's = 2,009,701 bp (0.01%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 62,637,212 number of insertions = 1,286,115 mapped reads with insertion percentage = 0.89% number of deletions = 1,276,757 mapped reads with deletion percentage = 0.88% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 4.5746X std coverageData = 5.5839X There is a 82.6% of reference with a coverageData >= 1X There is a 71.03% of reference with a coverageData >= 2X There is a 58.96% of reference with a coverageData >= 3X There is a 47.86% of reference with a coverageData >= 4X There is a 38.34% of reference with a coverageData >= 5X There is a 30.49% of reference with a coverageData >= 6X There is a 24.19% of reference with a coverageData >= 7X There is a 19.19% of reference with a coverageData >= 8X There is a 15.26% of reference with a coverageData >= 9X There is a 12.18% of reference with a coverageData >= 10X There is a 9.76% of reference with a coverageData >= 11X There is a 7.86% of reference with a coverageData >= 12X There is a 6.36% of reference with a coverageData >= 13X There is a 5.17% of reference with a coverageData >= 14X There is a 4.22% of reference with a coverageData >= 15X There is a 3.46% of reference with a coverageData >= 16X There is a 2.86% of reference with a coverageData >= 17X There is a 2.37% of reference with a coverageData >= 18X There is a 1.98% of reference with a coverageData >= 19X There is a 1.66% of reference with a coverageData >= 20X There is a 1.39% of reference with a coverageData >= 21X There is a 1.18% of reference with a coverageData >= 22X There is a 1% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.73% of reference with a coverageData >= 25X There is a 0.63% of reference with a coverageData >= 26X There is a 0.54% of reference with a coverageData >= 27X There is a 0.47% of reference with a coverageData >= 28X There is a 0.41% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1608036555 6.451484648457506 8.788987058209806 chr2 243199373 1125395539 4.627460692507624 5.484539169535641 chr3 198022430 918816406 4.639961271053991 4.5018474076762365 chr4 191154276 858390725 4.490565123429413 4.794635545105077 chr5 180915260 827555705 4.574272535108426 4.365120023885636 chr6 171115067 792680031 4.632438539149799 4.846242869698661 chr7 159138663 697850196 4.385170660884589 4.820745274573326 chr8 146364022 675328398 4.6140327983061304 4.564035279101698 chr9 141213431 549881150 3.893972025932859 5.397644386044852 chr10 135534747 746518461 5.507948902579203 7.59835551352636 chr11 135006516 618429790 4.580740310341762 4.697959142501943 chr12 133851895 914186711 6.829837642567556 6.394687993045209 chr13 115169878 413549976 3.5907824439998106 4.083970494180845 chr14 107349540 397309021 3.7010780018246936 4.3712773323168985 chr15 102531392 382034993 3.726029516891763 4.501998499552741 chr16 90354753 325785592 3.6056276087656394 4.580673773845345 chr17 81195210 301281087 3.7105771017773095 4.648414756497179 chr18 78077248 347893738 4.455763323010565 5.350503846830855 chr19 59128983 201942335 3.4152851064595513 5.322684522159258 chr20 63025520 270074342 4.28515848818066 5.17517293479911 chr21 48129895 160260019 3.3297396347945494 6.245067274625752 chr22 51304566 124290701 2.422605056243922 3.6673347112794716 chrMT 16571 731498 44.1432623257498 13.123702328195916 chrX 155270560 890487458 5.735069532820646 5.583810064463385 chrY 59373566 12954941 0.21819374972357228 2.283821604212071