BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1770535.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 396,743,888 number of mapped reads = 380,371,909 (95.87%) number of supplementary alignments = 396,716 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 191,859,218 number of mapped paired reads (second in pair) = 188,512,691 number of mapped paired reads (both in pair) = 375,137,522 number of mapped paired reads (singletons) = 5,234,387 number of mapped bases = 30,154,439,971 bp number of sequenced bases = 30,147,229,667 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,583,557 duplication rate = 7.21% >>>>>>> Insert size mean insert size = 26,514.0574 std insert size = 1,541,103.7183 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.1887 >>>>>>> ACTG content number of A's = 8,822,100,500 bp (29.26%) number of C's = 6,226,412,621 bp (20.65%) number of T's = 8,849,440,413 bp (29.35%) number of G's = 6,241,663,507 bp (20.7%) number of N's = 7,612,626 bp (0.03%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 151,541,661 number of insertions = 2,552,299 mapped reads with insertion percentage = 0.66% number of deletions = 3,336,082 mapped reads with deletion percentage = 0.86% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 9.7408X std coverageData = 99.6027X There is a 91.69% of reference with a coverageData >= 1X There is a 91.51% of reference with a coverageData >= 2X There is a 91.05% of reference with a coverageData >= 3X There is a 89.94% of reference with a coverageData >= 4X There is a 87.67% of reference with a coverageData >= 5X There is a 83.69% of reference with a coverageData >= 6X There is a 77.68% of reference with a coverageData >= 7X There is a 69.65% of reference with a coverageData >= 8X There is a 60.06% of reference with a coverageData >= 9X There is a 49.67% of reference with a coverageData >= 10X There is a 39.36% of reference with a coverageData >= 11X There is a 29.89% of reference with a coverageData >= 12X There is a 21.79% of reference with a coverageData >= 13X There is a 15.29% of reference with a coverageData >= 14X There is a 10.37% of reference with a coverageData >= 15X There is a 6.83% of reference with a coverageData >= 16X There is a 4.42% of reference with a coverageData >= 17X There is a 2.83% of reference with a coverageData >= 18X There is a 1.83% of reference with a coverageData >= 19X There is a 1.21% of reference with a coverageData >= 20X There is a 0.84% of reference with a coverageData >= 21X There is a 0.62% of reference with a coverageData >= 22X There is a 0.49% of reference with a coverageData >= 23X There is a 0.41% of reference with a coverageData >= 24X There is a 0.36% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.29% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2470711494 9.912559030294252 257.70791433360245 chr2 243199373 2574847202 10.587392435423753 72.53203267088837 chr3 198022430 1962878063 9.912402665698021 9.913105603005 chr4 191154276 1956412636 10.234731217835797 43.7682437122985 chr5 180915260 1792799114 9.909606928680311 8.258675730245653 chr6 171115067 1710777197 9.997817416043205 37.315071679741145 chr7 159138663 1638419847 10.295548649921734 86.71390170105094 chr8 146364022 1510116391 10.31753821987756 129.63392750244358 chr9 141213431 1265442772 8.961206898230524 92.35279788408808 chr10 135534747 1541501595 11.373478972148744 173.294131178382 chr11 135006516 1366192644 10.119457078649448 38.961757423083725 chr12 133851895 1326241911 9.90827893023106 9.912244384274679 chr13 115169878 950959732 8.257017794183996 6.0935311293756405 chr14 107349540 904344518 8.424298026801047 12.47100754497486 chr15 102531392 847873005 8.269399141679457 6.074060881653397 chr16 90354753 949945329 10.513507009420966 59.735781735370956 chr17 81195210 857269544 10.558129525128392 54.07850330503429 chr18 78077248 814902779 10.437135015312014 111.42157241301295 chr19 59128983 652272117 11.031343410726343 141.86159341728904 chr20 63025520 630595729 10.005403033564816 16.027919822358538 chr21 48129895 415257172 8.627842882266833 29.92398543176498 chr22 51304566 378022991 7.368213406190786 7.593768728495849 chrMT 16571 11558966 697.5418502202643 75.22869611700062 chrX 155270560 1539469116 9.914752133308465 23.64295115524106 chrY 59373566 85628107 1.442192422803104 55.99653088371468