BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976570.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 1,450,059,946 number of mapped reads = 1,431,436,063 (98.72%) number of supplementary alignments = 10,579,937 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 719,913,603 number of mapped paired reads (second in pair) = 711,522,460 number of mapped paired reads (both in pair) = 1,416,204,746 number of mapped paired reads (singletons) = 15,231,317 number of mapped bases = 137,548,828,321 bp number of sequenced bases = 137,523,455,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 497,956,342 duplication rate = 32.73% >>>>>>> Insert size mean insert size = 32,030.2785 std insert size = 1,707,835.7812 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 54.3159 >>>>>>> ACTG content number of A's = 41,292,383,849 bp (30.03%) number of C's = 27,301,187,453 bp (19.85%) number of T's = 41,283,356,785 bp (30.02%) number of G's = 27,525,513,213 bp (20.02%) number of N's = 121,014,240 bp (0.09%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 869,902,933 number of insertions = 14,545,526 mapped reads with insertion percentage = 1% number of deletions = 10,616,294 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 44.4323X std coverageData = 50.7458X There is a 91.61% of reference with a coverageData >= 1X There is a 90.81% of reference with a coverageData >= 2X There is a 89.92% of reference with a coverageData >= 3X There is a 88.93% of reference with a coverageData >= 4X There is a 87.86% of reference with a coverageData >= 5X There is a 86.72% of reference with a coverageData >= 6X There is a 85.51% of reference with a coverageData >= 7X There is a 84.25% of reference with a coverageData >= 8X There is a 82.94% of reference with a coverageData >= 9X There is a 81.6% of reference with a coverageData >= 10X There is a 80.23% of reference with a coverageData >= 11X There is a 78.83% of reference with a coverageData >= 12X There is a 77.41% of reference with a coverageData >= 13X There is a 75.98% of reference with a coverageData >= 14X There is a 74.54% of reference with a coverageData >= 15X There is a 73.1% of reference with a coverageData >= 16X There is a 71.65% of reference with a coverageData >= 17X There is a 70.2% of reference with a coverageData >= 18X There is a 68.76% of reference with a coverageData >= 19X There is a 67.32% of reference with a coverageData >= 20X There is a 65.9% of reference with a coverageData >= 21X There is a 64.49% of reference with a coverageData >= 22X There is a 63.09% of reference with a coverageData >= 23X There is a 61.7% of reference with a coverageData >= 24X There is a 60.34% of reference with a coverageData >= 25X There is a 58.99% of reference with a coverageData >= 26X There is a 57.65% of reference with a coverageData >= 27X There is a 56.34% of reference with a coverageData >= 28X There is a 55.05% of reference with a coverageData >= 29X There is a 53.78% of reference with a coverageData >= 30X There is a 52.53% of reference with a coverageData >= 31X There is a 51.3% of reference with a coverageData >= 32X There is a 50.09% of reference with a coverageData >= 33X There is a 48.91% of reference with a coverageData >= 34X There is a 47.74% of reference with a coverageData >= 35X There is a 46.6% of reference with a coverageData >= 36X There is a 45.49% of reference with a coverageData >= 37X There is a 44.39% of reference with a coverageData >= 38X There is a 43.32% of reference with a coverageData >= 39X There is a 42.27% of reference with a coverageData >= 40X There is a 41.25% of reference with a coverageData >= 41X There is a 40.24% of reference with a coverageData >= 42X There is a 39.26% of reference with a coverageData >= 43X There is a 38.3% of reference with a coverageData >= 44X There is a 37.36% of reference with a coverageData >= 45X There is a 36.45% of reference with a coverageData >= 46X There is a 35.55% of reference with a coverageData >= 47X There is a 34.67% of reference with a coverageData >= 48X There is a 33.82% of reference with a coverageData >= 49X There is a 32.99% of reference with a coverageData >= 50X There is a 32.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11572713616 46.430029219465816 72.17747178169628 chr2 243199373 12296465462 50.561254785800784 47.85869620970345 chr3 198022430 9437524690 47.65886717984422 43.08980979766415 chr4 191154276 9043548224 47.31020625455431 45.721621213754105 chr5 180915260 8885337159 49.11325423294862 44.03750066475091 chr6 171115067 8458765309 49.43319987713297 51.61280579622321 chr7 159138663 7306060039 45.91002526519907 44.436805237307325 chr8 146364022 7481793574 51.11770961035766 47.86485501251924 chr9 141213431 5908875020 41.84357662126345 53.372260546532026 chr10 135534747 6565441418 48.44102020568939 58.69181353246178 chr11 135006516 6362563679 47.1278266228276 48.0149822669766 chr12 133851895 6761774322 50.5168367022372 46.4443899559465 chr13 115169878 4635273219 40.24727037567931 42.8599297950847 chr14 107349540 4319468852 40.23742302016385 45.36007180572728 chr15 102531392 4423029582 43.13829643510545 47.525735732146096 chr16 90354753 3610730563 39.961711399952584 45.11064363638055 chr17 81195210 3700867779 45.579878160300346 60.99072341108629 chr18 78077248 3472681378 44.477507429565144 54.35316134625939 chr19 59128983 2212783610 37.422994574420464 54.354938460592564 chr20 63025520 2997869559 47.56596310510409 48.18675911347057 chr21 48129895 1740386842 36.160204421804785 57.77455995114298 chr22 51304566 1590055493 30.992475270134825 42.84747599459784 chrMT 16571 37117359 2239.8985577213202 533.957218670942 chrX 155270560 4086163669 26.316409685132843 31.198310021349105 chrY 59373566 641537904 10.805109869937743 29.98932936038074