BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779415.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 = 13,687,070 number of mapped reads = 13,006,103 (95.02%) number of supplementary alignments = 85,983 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,553,371 number of mapped paired reads (second in pair) = 6,452,732 number of mapped paired reads (both in pair) = 12,862,022 number of mapped paired reads (singletons) = 144,081 number of mapped bases = 1,032,692,234 bp number of sequenced bases = 1,032,477,966 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,281,437 duplication rate = 6.8% >>>>>>> Insert size mean insert size = 73,723.7415 std insert size = 2,556,715.3956 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 52.6541 >>>>>>> ACTG content number of A's = 323,781,973 bp (31.36%) number of C's = 191,993,145 bp (18.6%) number of T's = 319,359,253 bp (30.93%) number of G's = 197,121,093 bp (19.09%) number of N's = 222,502 bp (0.02%) GC percentage = 37.69% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 4,004,363 number of insertions = 97,925 mapped reads with insertion percentage = 0.75% number of deletions = 107,591 mapped reads with deletion percentage = 0.82% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.3336X std coverageData = 3.8468X There is a 11.12% of reference with a coverageData >= 1X There is a 5.52% of reference with a coverageData >= 2X There is a 3.36% of reference with a coverageData >= 3X There is a 2.29% of reference with a coverageData >= 4X There is a 1.65% of reference with a coverageData >= 5X There is a 1.25% of reference with a coverageData >= 6X There is a 0.98% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.63% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 51628773 0.2071359854305037 5.189564017510937 chr2 243199373 86244360 0.3546241050547445 6.401769727802567 chr3 198022430 86207160 0.4353403803801418 2.5542103170051584 chr4 191154276 68754500 0.35968068012247867 2.3144769003858334 chr5 180915260 99880963 0.5520869991840379 2.8290696156517416 chr6 171115067 61225028 0.3578003332693082 4.852879998556283 chr7 159138663 127772071 0.8028977282535043 5.573578412356165 chr8 146364022 43983060 0.3005045871177276 2.0543645001177566 chr9 141213431 57023059 0.4038076165715427 2.8513691839133752 chr10 135534747 26298546 0.19403545276843287 6.082737989295841 chr11 135006516 53717820 0.39789057292612456 1.9395164790365675 chr12 133851895 52620571 0.3931253345348603 2.074421171371616 chr13 115169878 40235462 0.34935751169242363 1.453707076509375 chr14 107349540 23826252 0.22195020118390818 4.903021882098446 chr15 102531392 15901701 0.15509104762763778 0.8613691496282527 chr16 90354753 15812686 0.17500668725197002 2.600604717327434 chr17 81195210 16239429 0.20000476629101643 1.7806026334498353 chr18 78077248 23811347 0.3049716480785798 2.7779630963315634 chr19 59128983 6789306 0.11482196472075293 3.658084136495202 chr20 63025520 13033616 0.20679902363360111 6.691190682348536 chr21 48129895 13405751 0.2785327289826832 1.4986688286966754 chr22 51304566 4763862 0.09285454242025944 0.6769881249963008 chrMT 16571 59544 3.593265343069217 2.735742283218436 chrX 155270560 37955388 0.24444677728991251 1.4105656023278124 chrY 59373566 5501979 0.09266714753161365 0.706866218799533