BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976572.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 = 262,196,872 number of mapped reads = 260,130,677 (99.21%) number of supplementary alignments = 8,788,071 (3.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 130,370,106 number of mapped paired reads (second in pair) = 129,760,571 number of mapped paired reads (both in pair) = 259,121,098 number of mapped paired reads (singletons) = 1,009,579 number of mapped bases = 57,248,545,345 bp number of sequenced bases = 57,228,883,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,488,008 duplication rate = 9.16% >>>>>>> Insert size mean insert size = 81,260.6289 std insert size = 2,755,531.3264 median insert size = 589 >>>>>>> Mapping quality mean mapping quality = 55.3865 >>>>>>> ACTG content number of A's = 16,630,828,412 bp (29.06%) number of C's = 11,967,542,296 bp (20.91%) number of T's = 16,536,236,239 bp (28.89%) number of G's = 12,092,480,453 bp (21.13%) number of N's = 1,795,877 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 534,049,673 number of insertions = 5,722,786 mapped reads with insertion percentage = 2.09% number of deletions = 7,057,790 mapped reads with deletion percentage = 2.58% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 18.493X std coverageData = 34.4353X There is a 91.75% of reference with a coverageData >= 1X There is a 90.85% of reference with a coverageData >= 2X There is a 89.59% of reference with a coverageData >= 3X There is a 87.91% of reference with a coverageData >= 4X There is a 85.82% of reference with a coverageData >= 5X There is a 83.34% of reference with a coverageData >= 6X There is a 80.5% of reference with a coverageData >= 7X There is a 77.37% of reference with a coverageData >= 8X There is a 74% of reference with a coverageData >= 9X There is a 70.46% of reference with a coverageData >= 10X There is a 66.81% of reference with a coverageData >= 11X There is a 63.12% of reference with a coverageData >= 12X There is a 59.43% of reference with a coverageData >= 13X There is a 55.79% of reference with a coverageData >= 14X There is a 52.24% of reference with a coverageData >= 15X There is a 48.8% of reference with a coverageData >= 16X There is a 45.5% of reference with a coverageData >= 17X There is a 42.35% of reference with a coverageData >= 18X There is a 39.37% of reference with a coverageData >= 19X There is a 36.55% of reference with a coverageData >= 20X There is a 33.9% of reference with a coverageData >= 21X There is a 31.43% of reference with a coverageData >= 22X There is a 29.12% of reference with a coverageData >= 23X There is a 26.97% of reference with a coverageData >= 24X There is a 24.97% of reference with a coverageData >= 25X There is a 23.12% of reference with a coverageData >= 26X There is a 21.41% of reference with a coverageData >= 27X There is a 19.82% of reference with a coverageData >= 28X There is a 18.36% of reference with a coverageData >= 29X There is a 17.01% of reference with a coverageData >= 30X There is a 15.77% of reference with a coverageData >= 31X There is a 14.62% of reference with a coverageData >= 32X There is a 13.56% of reference with a coverageData >= 33X There is a 12.58% of reference with a coverageData >= 34X There is a 11.68% of reference with a coverageData >= 35X There is a 10.85% of reference with a coverageData >= 36X There is a 10.09% of reference with a coverageData >= 37X There is a 9.39% of reference with a coverageData >= 38X There is a 8.74% of reference with a coverageData >= 39X There is a 8.14% of reference with a coverageData >= 40X There is a 7.58% of reference with a coverageData >= 41X There is a 7.07% of reference with a coverageData >= 42X There is a 6.6% of reference with a coverageData >= 43X There is a 6.17% of reference with a coverageData >= 44X There is a 5.76% of reference with a coverageData >= 45X There is a 5.39% of reference with a coverageData >= 46X There is a 5.04% of reference with a coverageData >= 47X There is a 4.72% of reference with a coverageData >= 48X There is a 4.43% of reference with a coverageData >= 49X There is a 4.15% of reference with a coverageData >= 50X There is a 3.9% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5118622496 20.53604711380037 62.117778557340145 chr2 243199373 4637088709 19.06702575668236 35.47691965059634 chr3 198022430 3650824297 18.436418020928237 15.835980723826902 chr4 191154276 3408853949 17.83299866648026 14.422686531053705 chr5 180915260 3464369933 19.14913055427165 15.02595231343896 chr6 171115067 3173572763 18.546425038071018 28.500624401358778 chr7 159138663 3123430447 19.627099965016043 18.95449035560673 chr8 146364022 2889909804 19.744673346022154 17.430337270920194 chr9 141213431 2465754643 17.461190663939043 65.33790382745545 chr10 135534747 2879954432 21.248827298877092 51.57226719670803 chr11 135006516 2796996495 20.717492591246486 26.731021548439664 chr12 133851895 2772858743 20.715872143610667 17.626879677191962 chr13 115169878 1710716838 14.853856474520187 12.912840436169722 chr14 107349540 1817962741 16.934983987821465 16.05664041119654 chr15 102531392 1728610083 16.859325220123804 16.33811451760755 chr16 90354753 1966413558 21.763255309878385 21.44252877642697 chr17 81195210 1986322040 24.463537196344465 60.496610847499795 chr18 78077248 1536273390 19.67632606620561 57.5350720877853 chr19 59128983 1472367063 24.900936703071658 43.63089003170567 chr20 63025520 1447570307 22.968002596408567 20.063175335715464 chr21 48129895 677577855 14.07810789946664 20.15836758752804 chr22 51304566 845879785 16.48741722130541 19.50763946963928 chrMT 16571 1043256 62.95673163961137 19.744436097538003 chrX 155270560 1402335606 9.031561462778262 10.230606288439022 chrY 59373566 273236112 4.601982505143788 20.74841807901469