BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779228.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 = 10,512,070 number of mapped reads = 10,210,900 (97.14%) number of supplementary alignments = 24,518 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,146,469 number of mapped paired reads (second in pair) = 5,064,431 number of mapped paired reads (both in pair) = 10,113,604 number of mapped paired reads (singletons) = 97,296 number of mapped bases = 812,415,553 bp number of sequenced bases = 812,262,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,529 duplication rate = 1.04% >>>>>>> Insert size mean insert size = 53,977.8498 std insert size = 2,192,968.3785 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.0062 >>>>>>> ACTG content number of A's = 248,422,619 bp (30.58%) number of C's = 157,035,974 bp (19.33%) number of T's = 246,167,196 bp (30.31%) number of G's = 160,483,553 bp (19.76%) number of N's = 153,545 bp (0.02%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,156,256 number of insertions = 58,268 mapped reads with insertion percentage = 0.57% number of deletions = 73,757 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 0.2624X std coverageData = 0.789X There is a 17.03% of reference with a coverageData >= 1X There is a 5.61% of reference with a coverageData >= 2X There is a 2.02% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 66414446 0.26645649159686546 1.0880487808767685 chr2 243199373 71299724 0.29317396307596566 0.7535878078580379 chr3 198022430 52049721 0.2628476026680412 0.7041188035924996 chr4 191154276 59998180 0.3138730728681162 0.769752224334238 chr5 180915260 47912258 0.26483259621106586 0.6953847949046337 chr6 171115067 54642519 0.31933201417032436 0.78765700850905 chr7 159138663 54982165 0.34549847261190075 0.9738637005113973 chr8 146364022 52548164 0.35902377703176264 0.8197500160788326 chr9 141213431 30688853 0.2173224797576089 0.6754707974441961 chr10 135534747 27302136 0.20144012221456392 1.1181236605968337 chr11 135006516 30969264 0.2293908836222394 0.6475433017628905 chr12 133851895 34647346 0.2588483786501491 0.70495456206145 chr13 115169878 31421958 0.2728313908607249 0.7097008146595504 chr14 107349540 28273074 0.26337396508638977 0.7268614684367288 chr15 102531392 19842527 0.19352635922469483 0.6106389984000247 chr16 90354753 14135547 0.1564449741786135 0.5276826678549854 chr17 81195210 16177358 0.19924030001277168 0.6353545988282215 chr18 78077248 20836885 0.2668752489841855 0.7362218446241565 chr19 59128983 7707923 0.13035778071812937 0.7223668471847533 chr20 63025520 14656477 0.232548291549201 0.6371523705285856 chr21 48129895 9382275 0.19493653580586454 0.604831461211709 chr22 51304566 4121755 0.08033895072808919 0.36207314413169434 chrMT 16571 240 0.014483133184478908 0.11947121844879441 chrX 155270560 61724114 0.39752618912432597 0.9191048594109695 chrY 59373566 680644 0.011463754762515023 0.14840521185185188