BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781851.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 162,472,042 number of mapped reads = 157,420,590 (96.89%) number of supplementary alignments = 528,609 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 79,524,103 number of mapped paired reads (second in pair) = 77,896,487 number of mapped paired reads (both in pair) = 153,908,934 number of mapped paired reads (singletons) = 3,511,656 number of mapped bases = 15,599,357,473 bp number of sequenced bases = 15,596,177,796 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,175,059 duplication rate = 6.87% >>>>>>> Insert size mean insert size = 45,961.9278 std insert size = 2,113,700.8677 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.8173 >>>>>>> ACTG content number of A's = 4,676,608,259 bp (29.99%) number of C's = 3,133,169,047 bp (20.09%) number of T's = 4,610,936,508 bp (29.56%) number of G's = 3,170,723,426 bp (20.33%) number of N's = 4,740,556 bp (0.03%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 70,663,904 number of insertions = 1,865,472 mapped reads with insertion percentage = 1.17% number of deletions = 1,405,189 mapped reads with deletion percentage = 0.88% homopolymer indels = 47.53% >>>>>>> Coverage mean coverageData = 5.0391X std coverageData = 6.2469X There is a 81.82% of reference with a coverageData >= 1X There is a 70.99% of reference with a coverageData >= 2X There is a 59.87% of reference with a coverageData >= 3X There is a 49.72% of reference with a coverageData >= 4X There is a 40.9% of reference with a coverageData >= 5X There is a 33.49% of reference with a coverageData >= 6X There is a 27.38% of reference with a coverageData >= 7X There is a 22.4% of reference with a coverageData >= 8X There is a 18.36% of reference with a coverageData >= 9X There is a 15.11% of reference with a coverageData >= 10X There is a 12.47% of reference with a coverageData >= 11X There is a 10.34% of reference with a coverageData >= 12X There is a 8.61% of reference with a coverageData >= 13X There is a 7.19% of reference with a coverageData >= 14X There is a 6.04% of reference with a coverageData >= 15X There is a 5.09% of reference with a coverageData >= 16X There is a 4.31% of reference with a coverageData >= 17X There is a 3.66% of reference with a coverageData >= 18X There is a 3.12% of reference with a coverageData >= 19X There is a 2.67% of reference with a coverageData >= 20X There is a 2.3% of reference with a coverageData >= 21X There is a 1.98% of reference with a coverageData >= 22X There is a 1.71% of reference with a coverageData >= 23X There is a 1.49% of reference with a coverageData >= 24X There is a 1.29% of reference with a coverageData >= 25X There is a 1.13% of reference with a coverageData >= 26X There is a 0.99% of reference with a coverageData >= 27X There is a 0.87% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.68% of reference with a coverageData >= 30X There is a 0.6% of reference with a coverageData >= 31X There is a 0.53% of reference with a coverageData >= 32X There is a 0.47% of reference with a coverageData >= 33X There is a 0.42% of reference with a coverageData >= 34X There is a 0.38% of reference with a coverageData >= 35X There is a 0.34% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1177662326 4.724812003577716 7.281099876442772 chr2 243199373 1854994071 7.627462390702791 8.123554201018388 chr3 198022430 1016830854 5.134927664507501 5.44514861607628 chr4 191154276 999794314 5.230300545304045 5.485198316835431 chr5 180915260 922787104 5.100659303145572 5.12205423629028 chr6 171115067 887420849 5.186105844203655 5.549704964175056 chr7 159138663 765150003 4.808071078239485 5.713903390953193 chr8 146364022 750436017 5.127189091592468 5.345593895941689 chr9 141213431 598396838 4.237534870178178 5.99351061034885 chr10 135534747 805705346 5.944640498720228 7.953162854441442 chr11 135006516 685611362 5.0783575660896245 5.502118207467913 chr12 133851895 999372546 7.466256237911312 7.536939936773185 chr13 115169878 476091261 4.133817533435262 4.926793277318844 chr14 107349540 448005641 4.173335451647022 5.162705814000264 chr15 102531392 403514840 3.9355248390658737 5.0378870577136174 chr16 90354753 332737926 3.6825724707586773 4.803949256427317 chr17 81195210 294773039 3.6304239991497034 4.832758103552589 chr18 78077248 372061633 4.765301576715409 5.517151198782114 chr19 59128983 186881581 3.160574924821555 5.128804620744891 chr20 63025520 275694589 4.374332635414987 6.147908727638296 chr21 48129895 173087878 3.5962654395984033 6.539463599038884 chr22 51304566 120341808 2.345635435255412 3.950502843232816 chrMT 16571 582547 35.154607446744315 10.229294581706158 chrX 155270560 1037734106 6.683392563277932 7.012862731598398 chrY 59373566 13688994 0.2305570462114403 2.3344755732213303