BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779413.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 = 17,624,788 number of mapped reads = 17,119,559 (97.13%) number of supplementary alignments = 73,599 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,618,415 number of mapped paired reads (second in pair) = 8,501,144 number of mapped paired reads (both in pair) = 16,970,576 number of mapped paired reads (singletons) = 148,983 number of mapped bases = 1,361,440,173 bp number of sequenced bases = 1,361,150,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 749,708 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 121,567.3516 std insert size = 3,278,501.6031 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.2423 >>>>>>> ACTG content number of A's = 414,060,461 bp (30.42%) number of C's = 266,660,917 bp (19.59%) number of T's = 406,582,049 bp (29.87%) number of G's = 273,544,130 bp (20.1%) number of N's = 303,314 bp (0.02%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,654,624 number of insertions = 123,911 mapped reads with insertion percentage = 0.72% number of deletions = 140,223 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.4398X std coverageData = 2.0911X There is a 22.3% of reference with a coverageData >= 1X There is a 9.55% of reference with a coverageData >= 2X There is a 4.53% of reference with a coverageData >= 3X There is a 2.36% of reference with a coverageData >= 4X There is a 1.33% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 110367638 0.44279784562703256 4.647564329835045 chr2 243199373 106084926 0.4362055900530632 1.0882197686063788 chr3 198022430 90519996 0.4571199131330729 1.0438013242156905 chr4 191154276 72954450 0.381652200131793 0.9505797128534166 chr5 180915260 121265170 0.6702871277967375 1.3098058233310217 chr6 171115067 72304719 0.42255027723537636 1.4864649661675438 chr7 159138663 171908891 1.080245917360761 4.973933410149787 chr8 146364022 63760009 0.4356262429027811 1.0426970217365978 chr9 141213431 89406691 0.6331316388736423 2.27694581171506 chr10 135534747 48628456 0.35878958773575603 1.531133613776769 chr11 135006516 82306656 0.6096495075837672 1.3667482254308827 chr12 133851895 52966570 0.39571027365731354 1.0109480442198409 chr13 115169878 42030569 0.36494411325155696 0.9279799406755178 chr14 107349540 35365098 0.32943874747856394 0.9326543475645072 chr15 102531392 30470599 0.2971831202681809 0.8516896207734498 chr16 90354753 22247328 0.2462220000756352 0.7698921725984652 chr17 81195210 19676910 0.24234077355055797 0.9183656735012949 chr18 78077248 38225784 0.48958928470429697 1.475426357884812 chr19 59128983 17835761 0.30164159934900286 2.5361096261096354 chr20 63025520 17321964 0.2748404773177595 0.8257293326151829 chr21 48129895 16944505 0.3520578010818432 1.004460480992149 chr22 51304566 11013609 0.21467112693244497 0.7368649898249644 chrMT 16571 1200 0.07241566592239454 0.392671782962338 chrX 155270560 20758639 0.133693335040461 0.582532003305581 chrY 59373566 7074035 0.11914451963353523 0.5557234725628104