BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779336.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 154,379,068 number of mapped reads = 148,805,103 (96.39%) number of supplementary alignments = 669,092 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 75,312,227 number of mapped paired reads (second in pair) = 73,492,876 number of mapped paired reads (both in pair) = 146,134,818 number of mapped paired reads (singletons) = 2,670,285 number of mapped bases = 14,754,519,400 bp number of sequenced bases = 14,751,112,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,565,484 duplication rate = 6.13% >>>>>>> Insert size mean insert size = 61,375.5295 std insert size = 2,465,407.1609 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 53.9158 >>>>>>> ACTG content number of A's = 4,371,936,456 bp (29.64%) number of C's = 2,991,747,760 bp (20.28%) number of T's = 4,349,266,487 bp (29.48%) number of G's = 3,037,467,954 bp (20.59%) number of N's = 693,829 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 58,989,486 number of insertions = 1,520,891 mapped reads with insertion percentage = 1% number of deletions = 1,541,172 mapped reads with deletion percentage = 1.02% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 4.7661X std coverageData = 8.2891X There is a 82.51% of reference with a coverageData >= 1X There is a 71.16% of reference with a coverageData >= 2X There is a 59.45% of reference with a coverageData >= 3X There is a 48.72% of reference with a coverageData >= 4X There is a 39.49% of reference with a coverageData >= 5X There is a 31.82% of reference with a coverageData >= 6X There is a 25.59% of reference with a coverageData >= 7X There is a 20.59% of reference with a coverageData >= 8X There is a 16.6% of reference with a coverageData >= 9X There is a 13.42% of reference with a coverageData >= 10X There is a 10.9% of reference with a coverageData >= 11X There is a 8.88% of reference with a coverageData >= 12X There is a 7.27% of reference with a coverageData >= 13X There is a 5.98% of reference with a coverageData >= 14X There is a 4.94% of reference with a coverageData >= 15X There is a 4.1% of reference with a coverageData >= 16X There is a 3.42% of reference with a coverageData >= 17X There is a 2.86% of reference with a coverageData >= 18X There is a 2.4% of reference with a coverageData >= 19X There is a 2.03% of reference with a coverageData >= 20X There is a 1.72% of reference with a coverageData >= 21X There is a 1.46% of reference with a coverageData >= 22X There is a 1.25% of reference with a coverageData >= 23X There is a 1.07% of reference with a coverageData >= 24X There is a 0.92% of reference with a coverageData >= 25X There is a 0.79% of reference with a coverageData >= 26X There is a 0.69% of reference with a coverageData >= 27X There is a 0.6% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.45% of reference with a coverageData >= 30X There is a 0.4% of reference with a coverageData >= 31X There is a 0.35% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1262268028 5.0642522892651085 7.833767748290067 chr2 243199373 1273589370 5.236811897537252 21.846072305528388 chr3 198022430 1013738799 5.1193129939876005 5.07520768072158 chr4 191154276 931137481 4.87113079803666 5.248169119857259 chr5 180915260 888478920 4.911022541713728 4.903303418727667 chr6 171115067 865282215 5.056727208013775 5.688299118583017 chr7 159138663 767840777 4.824979439471601 5.3316920305077415 chr8 146364022 741904350 5.06889835262931 5.219535211829919 chr9 141213431 597793464 4.233262089637918 5.828705218697054 chr10 135534747 842190016 6.213831025928724 7.882611370177299 chr11 135006516 683137842 5.060036080036315 5.361262387259762 chr12 133851895 681573549 5.091997756176705 5.9622003924589615 chr13 115169878 438630616 3.808553274667878 4.499488162056695 chr14 107349540 455589009 4.243977282063808 5.060265366345521 chr15 102531392 449358236 4.382640547784624 5.385966690632351 chr16 90354753 355560164 3.935157279440518 4.711753405761158 chr17 81195210 379222373 4.670501782063252 5.79062321855015 chr18 78077248 351758265 4.505259521954462 5.72641880874994 chr19 59128983 235962614 3.990642186421505 5.915547209134017 chr20 63025520 296030357 4.6969919010584915 5.583815171630441 chr21 48129895 173623473 3.6073935544633953 6.5844856737320185 chr22 51304566 153801621 2.997815457594944 4.4742034649069895 chrMT 16571 653071 39.41047613300344 10.482072581856222 chrX 155270560 902402802 5.811808767869453 5.963638973564135 chrY 59373566 12991988 0.2188177142669854 2.3229529478760917