BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264615.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 = 1,210,368,908 number of mapped reads = 1,204,965,061 (99.55%) number of supplementary alignments = 12,492,325 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 603,798,982 number of mapped paired reads (second in pair) = 601,166,079 number of mapped paired reads (both in pair) = 1,201,255,576 number of mapped paired reads (singletons) = 3,709,485 number of mapped bases = 119,666,304,525 bp number of sequenced bases = 119,638,931,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 434,207,487 duplication rate = 35.65% >>>>>>> Insert size mean insert size = 128,776.9652 std insert size = 3,443,563.9618 median insert size = 291 >>>>>>> Mapping quality mean mapping quality = 54.4232 >>>>>>> ACTG content number of A's = 36,919,191,518 bp (30.86%) number of C's = 22,774,203,692 bp (19.04%) number of T's = 36,793,065,877 bp (30.75%) number of G's = 23,088,869,193 bp (19.3%) number of N's = 63,600,917 bp (0.05%) GC percentage = 38.33% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 438,670,942 number of insertions = 12,683,478 mapped reads with insertion percentage = 1.04% number of deletions = 12,097,224 mapped reads with deletion percentage = 0.98% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 38.6557X std coverageData = 37.9184X There is a 90.45% of reference with a coverageData >= 1X There is a 88.98% of reference with a coverageData >= 2X There is a 87.52% of reference with a coverageData >= 3X There is a 86.06% of reference with a coverageData >= 4X There is a 84.6% of reference with a coverageData >= 5X There is a 83.12% of reference with a coverageData >= 6X There is a 81.65% of reference with a coverageData >= 7X There is a 80.17% of reference with a coverageData >= 8X There is a 78.69% of reference with a coverageData >= 9X There is a 77.22% of reference with a coverageData >= 10X There is a 75.75% of reference with a coverageData >= 11X There is a 74.28% of reference with a coverageData >= 12X There is a 72.82% of reference with a coverageData >= 13X There is a 71.36% of reference with a coverageData >= 14X There is a 69.91% of reference with a coverageData >= 15X There is a 68.47% of reference with a coverageData >= 16X There is a 67.04% of reference with a coverageData >= 17X There is a 65.62% of reference with a coverageData >= 18X There is a 64.21% of reference with a coverageData >= 19X There is a 62.82% of reference with a coverageData >= 20X There is a 61.44% of reference with a coverageData >= 21X There is a 60.07% of reference with a coverageData >= 22X There is a 58.72% of reference with a coverageData >= 23X There is a 57.39% of reference with a coverageData >= 24X There is a 56.07% of reference with a coverageData >= 25X There is a 54.77% of reference with a coverageData >= 26X There is a 53.49% of reference with a coverageData >= 27X There is a 52.22% of reference with a coverageData >= 28X There is a 50.97% of reference with a coverageData >= 29X There is a 49.74% of reference with a coverageData >= 30X There is a 48.53% of reference with a coverageData >= 31X There is a 47.34% of reference with a coverageData >= 32X There is a 46.17% of reference with a coverageData >= 33X There is a 45.02% of reference with a coverageData >= 34X There is a 43.88% of reference with a coverageData >= 35X There is a 42.77% of reference with a coverageData >= 36X There is a 41.68% of reference with a coverageData >= 37X There is a 40.61% of reference with a coverageData >= 38X There is a 39.55% of reference with a coverageData >= 39X There is a 38.52% of reference with a coverageData >= 40X There is a 37.51% of reference with a coverageData >= 41X There is a 36.52% of reference with a coverageData >= 42X There is a 35.55% of reference with a coverageData >= 43X There is a 34.6% of reference with a coverageData >= 44X There is a 33.67% of reference with a coverageData >= 45X There is a 32.76% of reference with a coverageData >= 46X There is a 31.87% of reference with a coverageData >= 47X There is a 31% of reference with a coverageData >= 48X There is a 30.15% of reference with a coverageData >= 49X There is a 29.32% of reference with a coverageData >= 50X There is a 28.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9537758370 38.26573563481713 40.18204068936024 chr2 243199373 10896124134 44.803257506753525 37.855891538567704 chr3 198022430 9211570848 46.51781542121264 37.84872203001881 chr4 191154276 9915951407 51.87407582240012 39.861007942308895 chr5 180915260 8587278070 47.46574761023476 38.4958256155509 chr6 171115067 7915811010 46.26016369441038 38.895611988972085 chr7 159138663 6777459121 42.58838797081008 39.03150188946112 chr8 146364022 6524579858 44.57775735351137 37.494367468613746 chr9 141213431 5097020074 36.09444256049554 39.82496931605603 chr10 135534747 5205817269 38.40946609064021 34.60490377288819 chr11 135006516 5599117654 41.472943824429926 39.27806102164825 chr12 133851895 5635748620 42.104361839628794 39.34631171866879 chr13 115169878 4654301192 40.412486952534586 38.45255837584565 chr14 107349540 3843333203 35.80204631524271 38.869502681314124 chr15 102531392 3261378588 31.808585881678074 37.9805850753183 chr16 90354753 2053653195 22.72877880591406 28.354536559012526 chr17 81195210 1905746274 23.47116626707413 27.447900873425873 chr18 78077248 3502074827 44.853973682576516 36.46750320024786 chr19 59128983 866598571 14.656070966077667 20.569828486010984 chr20 63025520 1898879357 30.128737644687423 35.52934544891331 chr21 48129895 1460837533 30.351978390977166 39.99273154933498 chr22 51304566 606835133 11.828092123418411 19.736107243269945 chrMT 16571 323684 19.53316034035363 7.418897284195691 chrX 155270560 4143210599 26.683813074416683 25.537240309615292 chrY 59373566 564895934 9.514266567718032 19.56888377582692