BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976568.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 = 366,229,658 number of mapped reads = 364,007,938 (99.39%) number of supplementary alignments = 13,874,846 (3.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,640,025 number of mapped paired reads (second in pair) = 181,367,913 number of mapped paired reads (both in pair) = 362,328,536 number of mapped paired reads (singletons) = 1,679,402 number of mapped bases = 84,207,400,818 bp number of sequenced bases = 84,176,818,574 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,748,210 duplication rate = 11.46% >>>>>>> Insert size mean insert size = 75,907.4405 std insert size = 2,663,817.4144 median insert size = 533 >>>>>>> Mapping quality mean mapping quality = 55.2798 >>>>>>> ACTG content number of A's = 24,382,628,822 bp (28.97%) number of C's = 17,657,219,057 bp (20.98%) number of T's = 24,240,272,130 bp (28.8%) number of G's = 17,893,291,175 bp (21.26%) number of N's = 3,407,390 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 607,878,609 number of insertions = 8,948,072 mapped reads with insertion percentage = 2.3% number of deletions = 10,681,774 mapped reads with deletion percentage = 2.77% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 27.2015X std coverageData = 76.4656X There is a 92.17% of reference with a coverageData >= 1X There is a 91.91% of reference with a coverageData >= 2X There is a 91.55% of reference with a coverageData >= 3X There is a 91.05% of reference with a coverageData >= 4X There is a 90.38% of reference with a coverageData >= 5X There is a 89.53% of reference with a coverageData >= 6X There is a 88.48% of reference with a coverageData >= 7X There is a 87.22% of reference with a coverageData >= 8X There is a 85.74% of reference with a coverageData >= 9X There is a 84.05% of reference with a coverageData >= 10X There is a 82.15% of reference with a coverageData >= 11X There is a 80.05% of reference with a coverageData >= 12X There is a 77.78% of reference with a coverageData >= 13X There is a 75.36% of reference with a coverageData >= 14X There is a 72.82% of reference with a coverageData >= 15X There is a 70.17% of reference with a coverageData >= 16X There is a 67.46% of reference with a coverageData >= 17X There is a 64.7% of reference with a coverageData >= 18X There is a 61.92% of reference with a coverageData >= 19X There is a 59.15% of reference with a coverageData >= 20X There is a 56.4% of reference with a coverageData >= 21X There is a 53.7% of reference with a coverageData >= 22X There is a 51.05% of reference with a coverageData >= 23X There is a 48.46% of reference with a coverageData >= 24X There is a 45.96% of reference with a coverageData >= 25X There is a 43.54% of reference with a coverageData >= 26X There is a 41.22% of reference with a coverageData >= 27X There is a 38.99% of reference with a coverageData >= 28X There is a 36.86% of reference with a coverageData >= 29X There is a 34.83% of reference with a coverageData >= 30X There is a 32.89% of reference with a coverageData >= 31X There is a 31.06% of reference with a coverageData >= 32X There is a 29.32% of reference with a coverageData >= 33X There is a 27.67% of reference with a coverageData >= 34X There is a 26.12% of reference with a coverageData >= 35X There is a 24.65% of reference with a coverageData >= 36X There is a 23.26% of reference with a coverageData >= 37X There is a 21.95% of reference with a coverageData >= 38X There is a 20.71% of reference with a coverageData >= 39X There is a 19.55% of reference with a coverageData >= 40X There is a 18.46% of reference with a coverageData >= 41X There is a 17.43% of reference with a coverageData >= 42X There is a 16.46% of reference with a coverageData >= 43X There is a 15.54% of reference with a coverageData >= 44X There is a 14.69% of reference with a coverageData >= 45X There is a 13.88% of reference with a coverageData >= 46X There is a 13.12% of reference with a coverageData >= 47X There is a 12.41% of reference with a coverageData >= 48X There is a 11.74% of reference with a coverageData >= 49X There is a 11.11% of reference with a coverageData >= 50X There is a 10.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8625360041 34.60516971390013 150.21241746190768 chr2 243199373 6235348152 25.638833172485192 51.62670121273289 chr3 198022430 5701825534 28.793836809294785 19.744409703578352 chr4 191154276 4446631843 23.262005622097618 21.22034342312839 chr5 180915260 4534819390 25.065986086524706 19.077130490288905 chr6 171115067 5177449633 30.257123021200698 53.307315710849636 chr7 159138663 3992009690 25.085102606398046 35.00134972228377 chr8 146364022 4250793379 29.042611161641897 31.435594931934194 chr9 141213431 3777830298 26.752627361628228 179.49876541633438 chr10 135534747 3856774534 28.455983571504362 99.7173433427138 chr11 135006516 4030679036 29.85544072554246 67.59579286294057 chr12 133851895 4191204162 31.312251216166942 23.453635098376203 chr13 115169878 2683437905 23.299824151936672 19.53717179923336 chr14 107349540 2778919677 25.886647273942675 23.673722903637707 chr15 102531392 2651871777 25.863998579088832 22.280962020638125 chr16 90354753 3160911012 34.98333963682021 39.58552138216677 chr17 81195210 2888992161 35.58082011241796 120.5003260456883 chr18 78077248 1945219579 24.914038709458612 146.75593990424426 chr19 59128983 2317529419 39.19447454389669 100.30086899065714 chr20 63025520 2030933175 32.223981253942846 27.649724670939527 chr21 48129895 1215327474 25.25098951493661 37.169579181137884 chr22 51304566 1411009288 27.50260645417018 30.752455202521514 chrMT 16571 2920738 176.25598937903567 58.76005186999401 chrX 155270560 1831510027 11.795603925174225 17.205893557254427 chrY 59373566 468092894 7.883860201356273 44.17925428292636