BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264617.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 = 1,172,435,648 number of mapped reads = 1,167,228,867 (99.56%) number of supplementary alignments = 13,421,394 (1.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 584,893,088 number of mapped paired reads (second in pair) = 582,335,779 number of mapped paired reads (both in pair) = 1,163,575,540 number of mapped paired reads (singletons) = 3,653,327 number of mapped bases = 115,865,413,515 bp number of sequenced bases = 115,838,958,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 421,797,886 duplication rate = 35.52% >>>>>>> Insert size mean insert size = 149,867.1026 std insert size = 3,702,551.2143 median insert size = 298 >>>>>>> Mapping quality mean mapping quality = 54.3465 >>>>>>> ACTG content number of A's = 35,748,606,110 bp (30.86%) number of C's = 22,038,223,322 bp (19.02%) number of T's = 35,626,540,986 bp (30.76%) number of G's = 22,360,273,234 bp (19.3%) number of N's = 65,314,603 bp (0.06%) GC percentage = 38.33% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 452,070,983 number of insertions = 12,280,898 mapped reads with insertion percentage = 1.04% number of deletions = 11,774,427 mapped reads with deletion percentage = 0.99% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 37.4279X std coverageData = 39.2738X There is a 89.89% of reference with a coverageData >= 1X There is a 88.06% of reference with a coverageData >= 2X There is a 86.28% of reference with a coverageData >= 3X There is a 84.54% of reference with a coverageData >= 4X There is a 82.83% of reference with a coverageData >= 5X There is a 81.15% of reference with a coverageData >= 6X There is a 79.48% of reference with a coverageData >= 7X There is a 77.84% of reference with a coverageData >= 8X There is a 76.22% of reference with a coverageData >= 9X There is a 74.61% of reference with a coverageData >= 10X There is a 73.02% of reference with a coverageData >= 11X There is a 71.44% of reference with a coverageData >= 12X There is a 69.89% of reference with a coverageData >= 13X There is a 68.35% of reference with a coverageData >= 14X There is a 66.84% of reference with a coverageData >= 15X There is a 65.34% of reference with a coverageData >= 16X There is a 63.87% of reference with a coverageData >= 17X There is a 62.41% of reference with a coverageData >= 18X There is a 60.98% of reference with a coverageData >= 19X There is a 59.57% of reference with a coverageData >= 20X There is a 58.18% of reference with a coverageData >= 21X There is a 56.81% of reference with a coverageData >= 22X There is a 55.47% of reference with a coverageData >= 23X There is a 54.15% of reference with a coverageData >= 24X There is a 52.85% of reference with a coverageData >= 25X There is a 51.57% of reference with a coverageData >= 26X There is a 50.31% of reference with a coverageData >= 27X There is a 49.08% of reference with a coverageData >= 28X There is a 47.87% of reference with a coverageData >= 29X There is a 46.68% of reference with a coverageData >= 30X There is a 45.52% of reference with a coverageData >= 31X There is a 44.38% of reference with a coverageData >= 32X There is a 43.26% of reference with a coverageData >= 33X There is a 42.17% of reference with a coverageData >= 34X There is a 41.09% of reference with a coverageData >= 35X There is a 40.04% of reference with a coverageData >= 36X There is a 39.02% of reference with a coverageData >= 37X There is a 38.01% of reference with a coverageData >= 38X There is a 37.03% of reference with a coverageData >= 39X There is a 36.07% of reference with a coverageData >= 40X There is a 35.13% of reference with a coverageData >= 41X There is a 34.21% of reference with a coverageData >= 42X There is a 33.31% of reference with a coverageData >= 43X There is a 32.44% of reference with a coverageData >= 44X There is a 31.58% of reference with a coverageData >= 45X There is a 30.75% of reference with a coverageData >= 46X There is a 29.93% of reference with a coverageData >= 47X There is a 29.14% of reference with a coverageData >= 48X There is a 28.36% of reference with a coverageData >= 49X There is a 27.6% of reference with a coverageData >= 50X There is a 26.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9319031825 37.38819902478799 42.36647417732313 chr2 243199373 10349841760 42.55702484890863 39.500203184449724 chr3 198022430 8581540877 43.33620629238819 38.7632479024224 chr4 191154276 9995959588 52.29262874558977 42.523016703330455 chr5 180915260 8222885953 45.4515885116601 39.78049422551903 chr6 171115067 7573273599 44.25836796125031 40.57104363661413 chr7 159138663 6495013184 40.81354625933988 40.352983185492995 chr8 146364022 6462509393 44.153674548517124 39.82786941002483 chr9 141213431 4911816447 34.782926894538804 41.75652815489384 chr10 135534747 4961487391 36.60675583804351 35.620065660307986 chr11 135006516 5337833604 39.537599829626004 40.747511052777305 chr12 133851895 5112341782 38.1940187100078 38.7450588971624 chr13 115169878 4717639883 40.96244577944243 40.76119624789237 chr14 107349540 3719254018 34.64620358876247 38.89422823833595 chr15 102531392 3180768801 31.02238971845813 38.65994747337776 chr16 90354753 2085489325 23.081124741716685 29.325056511090736 chr17 81195210 1945686007 23.96306391719413 30.015778991083728 chr18 78077248 3171217149 40.6164052938956 37.35832376240796 chr19 59128983 923655375 15.621025901967569 22.574970323470062 chr20 63025520 1769136332 28.070158437407578 36.40014557994305 chr21 48129895 1565548067 32.527560407102484 41.933087214831495 chr22 51304566 611627461 11.921501509241887 20.751007393328226 chrMT 16571 384192 23.18459960171384 9.287989686105707 chrX 155270560 4273163749 27.52075956317798 29.18127683635788 chrY 59373566 578307753 9.740155290655778 21.769712545849913