BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779347.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 = 332,989,276 number of mapped reads = 316,363,832 (95.01%) number of supplementary alignments = 2,107,669 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 159,612,870 number of mapped paired reads (second in pair) = 156,750,962 number of mapped paired reads (both in pair) = 310,501,004 number of mapped paired reads (singletons) = 5,862,828 number of mapped bases = 31,708,628,991 bp number of sequenced bases = 31,700,062,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,876,887 duplication rate = 10.61% >>>>>>> Insert size mean insert size = 67,364.8 std insert size = 2,515,676.428 median insert size = 296 >>>>>>> Mapping quality mean mapping quality = 54.0296 >>>>>>> ACTG content number of A's = 9,423,831,479 bp (29.73%) number of C's = 6,389,563,323 bp (20.16%) number of T's = 9,382,987,383 bp (29.6%) number of G's = 6,496,979,896 bp (20.5%) number of N's = 6,700,398 bp (0.02%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 126,154,238 number of insertions = 3,153,215 mapped reads with insertion percentage = 0.98% number of deletions = 3,848,165 mapped reads with deletion percentage = 1.19% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 10.2428X std coverageData = 33.6365X There is a 84.86% of reference with a coverageData >= 1X There is a 78.83% of reference with a coverageData >= 2X There is a 73% of reference with a coverageData >= 3X There is a 67.39% of reference with a coverageData >= 4X There is a 62.02% of reference with a coverageData >= 5X There is a 56.93% of reference with a coverageData >= 6X There is a 52.12% of reference with a coverageData >= 7X There is a 47.63% of reference with a coverageData >= 8X There is a 43.44% of reference with a coverageData >= 9X There is a 39.57% of reference with a coverageData >= 10X There is a 35.99% of reference with a coverageData >= 11X There is a 32.7% of reference with a coverageData >= 12X There is a 29.69% of reference with a coverageData >= 13X There is a 26.94% of reference with a coverageData >= 14X There is a 24.42% of reference with a coverageData >= 15X There is a 22.14% of reference with a coverageData >= 16X There is a 20.06% of reference with a coverageData >= 17X There is a 18.18% of reference with a coverageData >= 18X There is a 16.47% of reference with a coverageData >= 19X There is a 14.92% of reference with a coverageData >= 20X There is a 13.52% of reference with a coverageData >= 21X There is a 12.26% of reference with a coverageData >= 22X There is a 11.11% of reference with a coverageData >= 23X There is a 10.08% of reference with a coverageData >= 24X There is a 9.14% of reference with a coverageData >= 25X There is a 8.3% of reference with a coverageData >= 26X There is a 7.53% of reference with a coverageData >= 27X There is a 6.84% of reference with a coverageData >= 28X There is a 6.22% of reference with a coverageData >= 29X There is a 5.66% of reference with a coverageData >= 30X There is a 5.15% of reference with a coverageData >= 31X There is a 4.69% of reference with a coverageData >= 32X There is a 4.27% of reference with a coverageData >= 33X There is a 3.89% of reference with a coverageData >= 34X There is a 3.55% of reference with a coverageData >= 35X There is a 3.24% of reference with a coverageData >= 36X There is a 2.96% of reference with a coverageData >= 37X There is a 2.71% of reference with a coverageData >= 38X There is a 2.48% of reference with a coverageData >= 39X There is a 2.27% of reference with a coverageData >= 40X There is a 2.08% of reference with a coverageData >= 41X There is a 1.91% of reference with a coverageData >= 42X There is a 1.75% of reference with a coverageData >= 43X There is a 1.61% of reference with a coverageData >= 44X There is a 1.48% of reference with a coverageData >= 45X There is a 1.36% of reference with a coverageData >= 46X There is a 1.25% of reference with a coverageData >= 47X There is a 1.15% of reference with a coverageData >= 48X There is a 1.06% of reference with a coverageData >= 49X There is a 0.98% of reference with a coverageData >= 50X There is a 0.91% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2787303431 11.182734148533976 87.14526941337814 chr2 243199373 2317490565 9.52917985113391 18.90726850611471 chr3 198022430 1859300391 9.389342363892817 9.644773636138357 chr4 191154276 2257503385 11.809850306461364 11.61982482433382 chr5 180915260 1491158063 8.242301191176466 8.655670874919903 chr6 171115067 1751440437 10.235454233846047 17.231374495015302 chr7 159138663 2783609365 17.491722706002626 54.24854886076369 chr8 146364022 2474522999 16.906634329849176 15.202806122584619 chr9 141213431 1329618151 9.415663521411076 23.891904034120206 chr10 135534747 828164554 6.11034861783451 45.826891812148794 chr11 135006516 1356971209 10.051153449512022 12.702571994305643 chr12 133851895 1241808096 9.277478634127668 20.535017925422196 chr13 115169878 919588008 7.984622576399707 9.165349592756796 chr14 107349540 791959980 7.377395189583486 9.51431282837503 chr15 102531392 959010615 9.353336537165125 11.969825976897301 chr16 90354753 786948107 8.709537471703342 11.147061716856827 chr17 81195210 830446498 10.227776958763947 31.592995093631952 chr18 78077248 912643194 11.688977485476947 26.58103715918139 chr19 59128983 430823229 7.286159969976145 58.98264733487325 chr20 63025520 918575787 14.574664151918144 14.510388765916229 chr21 48129895 353491667 7.344534348142667 9.651464825561883 chr22 51304566 214447506 4.179891240089625 7.159379577288198 chrMT 16571 17322 1.0453201375897652 2.1980672483376744 chrX 155270560 2087862277 13.446607502413851 13.26253947724374 chrY 59373566 23924155 0.4029428685486063 4.530236313565743