BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779275.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 = 13,382,504 number of mapped reads = 13,059,878 (97.59%) number of supplementary alignments = 29,871 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,573,748 number of mapped paired reads (second in pair) = 6,486,130 number of mapped paired reads (both in pair) = 12,955,244 number of mapped paired reads (singletons) = 104,634 number of mapped bases = 1,039,404,518 bp number of sequenced bases = 1,039,202,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,023 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 42,876.5823 std insert size = 1,960,584.0524 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 52.906 >>>>>>> ACTG content number of A's = 319,868,782 bp (30.78%) number of C's = 198,380,470 bp (19.09%) number of T's = 318,805,763 bp (30.68%) number of G's = 201,950,923 bp (19.43%) number of N's = 196,671 bp (0.02%) GC percentage = 38.52% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 4,117,632 number of insertions = 76,789 mapped reads with insertion percentage = 0.58% number of deletions = 96,824 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.3358X std coverageData = 0.9895X There is a 19.66% of reference with a coverageData >= 1X There is a 7.3% of reference with a coverageData >= 2X There is a 3.1% of reference with a coverageData >= 3X There is a 1.46% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 38123206 0.15295129796286444 0.9034744999238635 chr2 243199373 112899274 0.464225185317398 1.0432409236426976 chr3 198022430 82211500 0.4151625651700164 0.9657022032061321 chr4 191154276 93853510 0.4909830528719117 1.025488331111731 chr5 180915260 68960915 0.3811779890762117 0.9107775617142497 chr6 171115067 25356958 0.14818658838499593 0.5283863216210939 chr7 159138663 102271668 0.6426575796982786 1.9493964170223772 chr8 146364022 69634494 0.47576237007206595 1.0181892244763022 chr9 141213431 39262245 0.2780347784340712 0.8189800159892878 chr10 135534747 24643648 0.18182531450772546 1.1465955013736566 chr11 135006516 54881965 0.4065134530247414 1.0038577200414527 chr12 133851895 45165123 0.33742610069136486 0.8693330494010325 chr13 115169878 37281052 0.3237048840148984 0.8473979290671114 chr14 107349540 36875187 0.3435057756186007 0.8748745217269355 chr15 102531392 24938554 0.24322847387071464 0.7116728431228166 chr16 90354753 16344155 0.18088871318147481 0.593635905579285 chr17 81195210 13233145 0.1629793801875751 0.640464607465453 chr18 78077248 31669773 0.40562102035153696 0.9628682079907731 chr19 59128983 9434013 0.15954972538594145 0.6939003910888369 chr20 63025520 20667427 0.32792156256703636 0.8936315746173406 chr21 48129895 11378483 0.2364119639155664 0.7641346433870145 chr22 51304566 4214072 0.08213834222864297 0.3914817360801552 chrMT 16571 1245 0.07513125339448434 0.3097067422894312 chrX 155270560 75359407 0.48534253370374913 1.058779502642571 chrY 59373566 743499 0.012522390856564014 0.16859548017443424