BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779419.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 14,248,636 number of mapped reads = 13,743,137 (96.45%) number of supplementary alignments = 48,792 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,937,391 number of mapped paired reads (second in pair) = 6,805,746 number of mapped paired reads (both in pair) = 13,584,552 number of mapped paired reads (singletons) = 158,585 number of mapped bases = 1,092,529,825 bp number of sequenced bases = 1,092,302,236 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,298 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 191,367.517 std insert size = 4,203,064.633 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.2764 >>>>>>> ACTG content number of A's = 331,894,097 bp (30.38%) number of C's = 214,847,360 bp (19.67%) number of T's = 324,656,401 bp (29.72%) number of G's = 220,663,971 bp (20.2%) number of N's = 240,407 bp (0.02%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,589,831 number of insertions = 96,445 mapped reads with insertion percentage = 0.7% number of deletions = 110,639 mapped reads with deletion percentage = 0.79% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.3529X std coverageData = 1.1479X There is a 21.78% of reference with a coverageData >= 1X There is a 7.61% of reference with a coverageData >= 2X There is a 2.83% of reference with a coverageData >= 3X There is a 1.18% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 78948242 0.31674240843716894 2.036096683434348 chr2 243199373 86765556 0.35676718623777043 0.8490090964701086 chr3 198022430 77939250 0.39358798899700403 0.8361653345082172 chr4 191154276 55788332 0.2918497726935494 0.7010589696895719 chr5 180915260 121114998 0.6694570596200674 1.0865744796421255 chr6 171115067 51161113 0.2989866053116176 1.0866058018150724 chr7 159138663 110327711 0.6932803689572282 1.8216881867793662 chr8 146364022 46882229 0.3203125218846473 0.756364607092833 chr9 141213431 71782187 0.5083240771906463 1.7736370512490873 chr10 135534747 24513353 0.18086397431353896 1.3947713711791079 chr11 135006516 49041185 0.36325050414603693 0.883284800377123 chr12 133851895 42542314 0.31783124176165006 0.7502119736268845 chr13 115169878 38138610 0.33115091083104214 0.7713451524590943 chr14 107349540 34646552 0.3227452302077866 0.7653155296362569 chr15 102531392 24975514 0.24358894883627447 0.6930969635708024 chr16 90354753 19541478 0.21627504200028083 0.6415051249313113 chr17 81195210 33651255 0.41444877105435163 1.08669158342833 chr18 78077248 24130432 0.3090584340267731 1.0043368588101809 chr19 59128983 14270810 0.24135050656968005 1.365334818980204 chr20 63025520 20892133 0.3314868802351809 0.7658934664026783 chr21 48129895 12965798 0.26939177822847943 0.7235652078157091 chr22 51304566 11168373 0.21768770054501582 0.6641350191805875 chrMT 16571 1309 0.07899342224367871 0.37397679773037107 chrX 155270560 39322760 0.2532531601612051 0.6745449638614808 chrY 59373566 2018331 0.03399376416097359 0.2874816098240934