BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976573.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 = 289,372,162 number of mapped reads = 280,299,019 (96.86%) number of supplementary alignments = 8,630,995 (2.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 143,948,708 number of mapped paired reads (second in pair) = 136,350,311 number of mapped paired reads (both in pair) = 272,377,630 number of mapped paired reads (singletons) = 7,921,389 number of mapped bases = 57,380,509,162 bp number of sequenced bases = 57,361,005,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,792,456 duplication rate = 9.55% >>>>>>> Insert size mean insert size = 77,928.7609 std insert size = 2,706,900.4271 median insert size = 557 >>>>>>> Mapping quality mean mapping quality = 55.1935 >>>>>>> ACTG content number of A's = 16,548,524,025 bp (28.85%) number of C's = 12,098,563,434 bp (21.09%) number of T's = 16,404,770,228 bp (28.6%) number of G's = 12,240,664,326 bp (21.34%) number of N's = 68,483,343 bp (0.12%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 577,245,187 number of insertions = 5,707,998 mapped reads with insertion percentage = 1.93% number of deletions = 7,018,063 mapped reads with deletion percentage = 2.38% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 18.5356X std coverageData = 36.9773X There is a 91.87% of reference with a coverageData >= 1X There is a 91.08% of reference with a coverageData >= 2X There is a 89.91% of reference with a coverageData >= 3X There is a 88.29% of reference with a coverageData >= 4X There is a 86.22% of reference with a coverageData >= 5X There is a 83.71% of reference with a coverageData >= 6X There is a 80.8% of reference with a coverageData >= 7X There is a 77.57% of reference with a coverageData >= 8X There is a 74.08% of reference with a coverageData >= 9X There is a 70.41% of reference with a coverageData >= 10X There is a 66.65% of reference with a coverageData >= 11X There is a 62.85% of reference with a coverageData >= 12X There is a 59.07% of reference with a coverageData >= 13X There is a 55.35% of reference with a coverageData >= 14X There is a 51.75% of reference with a coverageData >= 15X There is a 48.27% of reference with a coverageData >= 16X There is a 44.96% of reference with a coverageData >= 17X There is a 41.81% of reference with a coverageData >= 18X There is a 38.84% of reference with a coverageData >= 19X There is a 36.04% of reference with a coverageData >= 20X There is a 33.43% of reference with a coverageData >= 21X There is a 30.99% of reference with a coverageData >= 22X There is a 28.72% of reference with a coverageData >= 23X There is a 26.62% of reference with a coverageData >= 24X There is a 24.67% of reference with a coverageData >= 25X There is a 22.86% of reference with a coverageData >= 26X There is a 21.2% of reference with a coverageData >= 27X There is a 19.66% of reference with a coverageData >= 28X There is a 18.24% of reference with a coverageData >= 29X There is a 16.92% of reference with a coverageData >= 30X There is a 15.71% of reference with a coverageData >= 31X There is a 14.6% of reference with a coverageData >= 32X There is a 13.57% of reference with a coverageData >= 33X There is a 12.62% of reference with a coverageData >= 34X There is a 11.75% of reference with a coverageData >= 35X There is a 10.94% of reference with a coverageData >= 36X There is a 10.19% of reference with a coverageData >= 37X There is a 9.51% of reference with a coverageData >= 38X There is a 8.87% of reference with a coverageData >= 39X There is a 8.28% of reference with a coverageData >= 40X There is a 7.74% of reference with a coverageData >= 41X There is a 7.23% of reference with a coverageData >= 42X There is a 6.77% of reference with a coverageData >= 43X There is a 6.33% of reference with a coverageData >= 44X There is a 5.93% of reference with a coverageData >= 45X There is a 5.56% of reference with a coverageData >= 46X There is a 5.21% of reference with a coverageData >= 47X There is a 4.89% of reference with a coverageData >= 48X There is a 4.6% of reference with a coverageData >= 49X There is a 4.32% of reference with a coverageData >= 50X There is a 4.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5059716420 20.29971439870555 69.77014073250713 chr2 243199373 4845635383 19.92453896252438 35.694660535900134 chr3 198022430 3756194442 18.968530191251567 16.00009406101569 chr4 191154276 3116384583 16.30298127884934 13.504529116289481 chr5 180915260 3333948378 18.428231968933964 15.008736821830064 chr6 171115067 3195916365 18.677001511503367 30.224901787276178 chr7 159138663 3075391887 19.325233912515653 21.540966767362814 chr8 146364022 2776096908 18.967071757566213 17.843740331070148 chr9 141213431 2493405492 17.65699958101011 69.20161827038567 chr10 135534747 2832372982 20.89776271172735 52.88195681009976 chr11 135006516 2770007324 20.517582455057205 29.04448667163146 chr12 133851895 2769995038 20.694477564176434 17.97539805811471 chr13 115169878 1662953189 14.439133025737858 12.906823063520996 chr14 107349540 1786056500 16.637765751022314 16.135650043253342 chr15 102531392 1894487157 18.47714265890392 17.662721835240696 chr16 90354753 2024971019 22.411339213112562 22.21866328109346 chr17 81195210 2137967738 26.33120522750049 59.029100641263916 chr18 78077248 1475021265 18.89181935562073 67.56667939279329 chr19 59128983 1515476084 25.630004223140453 51.87856039976919 chr20 63025520 1489813100 23.63825161617072 20.25747850338444 chr21 48129895 723379711 15.029737983014506 20.88222269382096 chr22 51304566 962535891 18.761213007824683 21.65701999275609 chrMT 16571 747221 45.09208858849798 14.065635723216227 chrX 155270560 1413037957 9.100488572978676 12.386456320931657 chrY 59373566 268997128 4.530587366101608 23.75543040261019