BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779350.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 = 312,671,364 number of mapped reads = 295,822,035 (94.61%) number of supplementary alignments = 1,374,748 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 148,818,795 number of mapped paired reads (second in pair) = 147,003,240 number of mapped paired reads (both in pair) = 291,300,724 number of mapped paired reads (singletons) = 4,521,311 number of mapped bases = 29,636,094,887 bp number of sequenced bases = 29,628,901,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,861,351 duplication rate = 18.51% >>>>>>> Insert size mean insert size = 73,636.5457 std insert size = 2,605,792.4178 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 53.7429 >>>>>>> ACTG content number of A's = 8,991,400,709 bp (30.35%) number of C's = 5,818,410,943 bp (19.64%) number of T's = 8,889,800,316 bp (30%) number of G's = 5,920,864,296 bp (19.98%) number of N's = 8,425,419 bp (0.03%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 103,064,139 number of insertions = 2,502,823 mapped reads with insertion percentage = 0.83% number of deletions = 3,205,837 mapped reads with deletion percentage = 1.06% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 9.5733X std coverageData = 27.4127X There is a 64.26% of reference with a coverageData >= 1X There is a 53.88% of reference with a coverageData >= 2X There is a 47.05% of reference with a coverageData >= 3X There is a 42.06% of reference with a coverageData >= 4X There is a 38.1% of reference with a coverageData >= 5X There is a 34.83% of reference with a coverageData >= 6X There is a 32.05% of reference with a coverageData >= 7X There is a 29.65% of reference with a coverageData >= 8X There is a 27.53% of reference with a coverageData >= 9X There is a 25.65% of reference with a coverageData >= 10X There is a 23.97% of reference with a coverageData >= 11X There is a 22.45% of reference with a coverageData >= 12X There is a 21.08% of reference with a coverageData >= 13X There is a 19.82% of reference with a coverageData >= 14X There is a 18.67% of reference with a coverageData >= 15X There is a 17.61% of reference with a coverageData >= 16X There is a 16.64% of reference with a coverageData >= 17X There is a 15.74% of reference with a coverageData >= 18X There is a 14.9% of reference with a coverageData >= 19X There is a 14.13% of reference with a coverageData >= 20X There is a 13.41% of reference with a coverageData >= 21X There is a 12.73% of reference with a coverageData >= 22X There is a 12.1% of reference with a coverageData >= 23X There is a 11.52% of reference with a coverageData >= 24X There is a 10.97% of reference with a coverageData >= 25X There is a 10.45% of reference with a coverageData >= 26X There is a 9.96% of reference with a coverageData >= 27X There is a 9.51% of reference with a coverageData >= 28X There is a 9.08% of reference with a coverageData >= 29X There is a 8.68% of reference with a coverageData >= 30X There is a 8.3% of reference with a coverageData >= 31X There is a 7.94% of reference with a coverageData >= 32X There is a 7.6% of reference with a coverageData >= 33X There is a 7.28% of reference with a coverageData >= 34X There is a 6.98% of reference with a coverageData >= 35X There is a 6.69% of reference with a coverageData >= 36X There is a 6.42% of reference with a coverageData >= 37X There is a 6.16% of reference with a coverageData >= 38X There is a 5.92% of reference with a coverageData >= 39X There is a 5.68% of reference with a coverageData >= 40X There is a 5.46% of reference with a coverageData >= 41X There is a 5.25% of reference with a coverageData >= 42X There is a 5.05% of reference with a coverageData >= 43X There is a 4.86% of reference with a coverageData >= 44X There is a 4.68% of reference with a coverageData >= 45X There is a 4.51% of reference with a coverageData >= 46X There is a 4.34% of reference with a coverageData >= 47X There is a 4.18% of reference with a coverageData >= 48X There is a 4.03% of reference with a coverageData >= 49X There is a 3.89% of reference with a coverageData >= 50X There is a 3.75% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2166119234 8.690526929519667 29.478645674946968 chr2 243199373 2098643858 8.629314426727571 19.880878984867163 chr3 198022430 2179331597 11.005478505642012 20.513608754084764 chr4 191154276 1884339002 9.857686897885559 19.439560088170115 chr5 180915260 1767989256 9.772471686468018 19.612847571475903 chr6 171115067 2004478429 11.714213506400345 22.35945352601932 chr7 159138663 2391294638 15.026484406243881 72.73441848870283 chr8 146364022 2409236731 16.460580257899718 27.590352516379806 chr9 141213431 1533551359 10.859812329041137 23.7190810205155 chr10 135534747 653808949 4.823921270904796 35.463696954340044 chr11 135006516 1154339919 8.550253374437126 18.602369567944073 chr12 133851895 1356649615 10.135453181294146 22.471429762240398 chr13 115169878 837114830 7.268522330118297 17.208080307656797 chr14 107349540 1022412901 9.524147946977696 20.222716234018698 chr15 102531392 840562223 8.198096276699335 19.231047453540615 chr16 90354753 832806597 9.217075686101428 19.528430035322604 chr17 81195210 639365323 7.874421693102339 17.919347631517827 chr18 78077248 554003550 7.095582441635238 17.214151041868355 chr19 59128983 431536618 7.298224933109369 19.53405083151261 chr20 63025520 554780160 8.8024685873278 18.393959034546626 chr21 48129895 316821337 6.582630961484541 16.41512372507608 chr22 51304566 218467893 4.258254382270771 10.572691035320016 chrMT 16571 199333 12.029026612757226 5.4765208554835 chrX 155270560 1772281284 11.414148850883258 24.932899989923563 chrY 59373566 15960251 0.2688107195717367 2.704528636666859