BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264626.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,231,064,828 number of mapped reads = 1,225,179,454 (99.52%) number of supplementary alignments = 9,211,003 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 614,119,858 number of mapped paired reads (second in pair) = 611,059,596 number of mapped paired reads (both in pair) = 1,221,109,644 number of mapped paired reads (singletons) = 4,069,810 number of mapped bases = 123,044,938,938 bp number of sequenced bases = 123,016,520,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 391,075,229 duplication rate = 31.59% >>>>>>> Insert size mean insert size = 108,345.4153 std insert size = 3,159,743.6239 median insert size = 342 >>>>>>> Mapping quality mean mapping quality = 54.5139 >>>>>>> ACTG content number of A's = 38,011,180,942 bp (30.9%) number of C's = 23,446,176,046 bp (19.06%) number of T's = 37,901,214,374 bp (30.81%) number of G's = 23,639,175,923 bp (19.22%) number of N's = 18,772,779 bp (0.02%) GC percentage = 38.28% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 421,035,941 number of insertions = 13,486,344 mapped reads with insertion percentage = 1.09% number of deletions = 12,715,975 mapped reads with deletion percentage = 1.02% homopolymer indels = 48.55% >>>>>>> Coverage mean coverageData = 39.7471X std coverageData = 38.8196X There is a 90.61% of reference with a coverageData >= 1X There is a 89.16% of reference with a coverageData >= 2X There is a 87.74% of reference with a coverageData >= 3X There is a 86.33% of reference with a coverageData >= 4X There is a 84.9% of reference with a coverageData >= 5X There is a 83.48% of reference with a coverageData >= 6X There is a 82.05% of reference with a coverageData >= 7X There is a 80.62% of reference with a coverageData >= 8X There is a 79.2% of reference with a coverageData >= 9X There is a 77.77% of reference with a coverageData >= 10X There is a 76.35% of reference with a coverageData >= 11X There is a 74.93% of reference with a coverageData >= 12X There is a 73.51% of reference with a coverageData >= 13X There is a 72.11% of reference with a coverageData >= 14X There is a 70.71% of reference with a coverageData >= 15X There is a 69.32% of reference with a coverageData >= 16X There is a 67.93% of reference with a coverageData >= 17X There is a 66.56% of reference with a coverageData >= 18X There is a 65.2% of reference with a coverageData >= 19X There is a 63.85% of reference with a coverageData >= 20X There is a 62.51% of reference with a coverageData >= 21X There is a 61.18% of reference with a coverageData >= 22X There is a 59.86% of reference with a coverageData >= 23X There is a 58.56% of reference with a coverageData >= 24X There is a 57.27% of reference with a coverageData >= 25X There is a 55.99% of reference with a coverageData >= 26X There is a 54.73% of reference with a coverageData >= 27X There is a 53.49% of reference with a coverageData >= 28X There is a 52.26% of reference with a coverageData >= 29X There is a 51.04% of reference with a coverageData >= 30X There is a 49.84% of reference with a coverageData >= 31X There is a 48.66% of reference with a coverageData >= 32X There is a 47.5% of reference with a coverageData >= 33X There is a 46.35% of reference with a coverageData >= 34X There is a 45.23% of reference with a coverageData >= 35X There is a 44.12% of reference with a coverageData >= 36X There is a 43.03% of reference with a coverageData >= 37X There is a 41.95% of reference with a coverageData >= 38X There is a 40.9% of reference with a coverageData >= 39X There is a 39.87% of reference with a coverageData >= 40X There is a 38.85% of reference with a coverageData >= 41X There is a 37.86% of reference with a coverageData >= 42X There is a 36.88% of reference with a coverageData >= 43X There is a 35.93% of reference with a coverageData >= 44X There is a 34.99% of reference with a coverageData >= 45X There is a 34.08% of reference with a coverageData >= 46X There is a 33.18% of reference with a coverageData >= 47X There is a 32.3% of reference with a coverageData >= 48X There is a 31.44% of reference with a coverageData >= 49X There is a 30.6% of reference with a coverageData >= 50X There is a 29.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9571661818 38.401757153495716 39.93196872680151 chr2 243199373 11282247124 46.39093836808535 39.854412187300376 chr3 198022430 9632722984 48.64460548231834 39.17777189367373 chr4 191154276 10029711330 52.46919681775782 40.008158444066794 chr5 180915260 8732480871 48.26834878937244 38.38450914998954 chr6 171115067 8307701955 48.5503825037219 40.40115167230905 chr7 159138663 6860080649 43.10756744889832 39.26947199025883 chr8 146364022 6945930498 47.4565429610837 39.50147463624672 chr9 141213431 5084566997 36.00625635248534 39.98471459055274 chr10 135534747 5233195115 38.61146481499685 34.6963793638273 chr11 135006516 5837434344 43.238167437785 39.69318076928269 chr12 133851895 6012894727 44.92199925148613 42.03837040198433 chr13 115169878 4800278287 41.67998065431657 38.75146808486148 chr14 107349540 3978141549 37.05783507782148 39.195649221079236 chr15 102531392 3395044825 33.11224746661003 38.36174345362994 chr16 90354753 2269071254 25.112915244204142 29.962064159548284 chr17 81195210 1943785097 23.93965231446535 28.44915038517861 chr18 78077248 3706033627 47.46624300846259 39.242580863698 chr19 59128983 840137142 14.208550517434064 20.46161543704234 chr20 63025520 1880034760 29.82973817590081 36.37907961132654 chr21 48129895 1539112366 31.978303006894155 40.22243586621129 chr22 51304566 656707785 12.80018205397157 21.18438636010679 chrMT 16571 45234 2.729708526944662 7.730600902730713 chrX 155270560 3935051612 25.34319198694202 25.36560359141944 chrY 59373566 570866988 9.614834116583127 20.850115418205498