BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976571.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 1,400,564,016 number of mapped reads = 1,379,368,729 (98.49%) number of supplementary alignments = 10,645,454 (0.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 694,985,772 number of mapped paired reads (second in pair) = 684,382,957 number of mapped paired reads (both in pair) = 1,362,152,434 number of mapped paired reads (singletons) = 17,216,295 number of mapped bases = 131,943,323,386 bp number of sequenced bases = 131,917,370,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 491,321,098 duplication rate = 32.92% >>>>>>> Insert size mean insert size = 32,246.5917 std insert size = 1,701,420.5634 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 54.2554 >>>>>>> ACTG content number of A's = 39,626,489,610 bp (30.04%) number of C's = 26,241,010,997 bp (19.89%) number of T's = 39,699,264,544 bp (30.09%) number of G's = 26,214,788,866 bp (19.87%) number of N's = 135,816,238 bp (0.1%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,283,244,741 number of insertions = 14,584,493 mapped reads with insertion percentage = 1.04% number of deletions = 10,960,240 mapped reads with deletion percentage = 0.78% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 42.6216X std coverageData = 56.7925X There is a 91.35% of reference with a coverageData >= 1X There is a 90.23% of reference with a coverageData >= 2X There is a 88.98% of reference with a coverageData >= 3X There is a 87.64% of reference with a coverageData >= 4X There is a 86.22% of reference with a coverageData >= 5X There is a 84.73% of reference with a coverageData >= 6X There is a 83.2% of reference with a coverageData >= 7X There is a 81.64% of reference with a coverageData >= 8X There is a 80.04% of reference with a coverageData >= 9X There is a 78.44% of reference with a coverageData >= 10X There is a 76.83% of reference with a coverageData >= 11X There is a 75.22% of reference with a coverageData >= 12X There is a 73.61% of reference with a coverageData >= 13X There is a 72% of reference with a coverageData >= 14X There is a 70.41% of reference with a coverageData >= 15X There is a 68.84% of reference with a coverageData >= 16X There is a 67.28% of reference with a coverageData >= 17X There is a 65.74% of reference with a coverageData >= 18X There is a 64.22% of reference with a coverageData >= 19X There is a 62.73% of reference with a coverageData >= 20X There is a 61.27% of reference with a coverageData >= 21X There is a 59.83% of reference with a coverageData >= 22X There is a 58.41% of reference with a coverageData >= 23X There is a 57.03% of reference with a coverageData >= 24X There is a 55.67% of reference with a coverageData >= 25X There is a 54.34% of reference with a coverageData >= 26X There is a 53.04% of reference with a coverageData >= 27X There is a 51.77% of reference with a coverageData >= 28X There is a 50.53% of reference with a coverageData >= 29X There is a 49.31% of reference with a coverageData >= 30X There is a 48.12% of reference with a coverageData >= 31X There is a 46.96% of reference with a coverageData >= 32X There is a 45.82% of reference with a coverageData >= 33X There is a 44.71% of reference with a coverageData >= 34X There is a 43.63% of reference with a coverageData >= 35X There is a 42.57% of reference with a coverageData >= 36X There is a 41.54% of reference with a coverageData >= 37X There is a 40.54% of reference with a coverageData >= 38X There is a 39.55% of reference with a coverageData >= 39X There is a 38.6% of reference with a coverageData >= 40X There is a 37.66% of reference with a coverageData >= 41X There is a 36.75% of reference with a coverageData >= 42X There is a 35.87% of reference with a coverageData >= 43X There is a 35% of reference with a coverageData >= 44X There is a 34.16% of reference with a coverageData >= 45X There is a 33.33% of reference with a coverageData >= 46X There is a 32.53% of reference with a coverageData >= 47X There is a 31.75% of reference with a coverageData >= 48X There is a 30.99% of reference with a coverageData >= 49X There is a 30.24% of reference with a coverageData >= 50X There is a 29.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11500829290 46.1416274264769 89.7831320180662 chr2 243199373 11235890512 46.200326807585974 51.3712224336988 chr3 198022430 9161599357 46.26546274076124 46.51262740473165 chr4 191154276 8664173641 45.325554951226934 49.341647297214756 chr5 180915260 8588933060 47.474895484217306 46.68930671391491 chr6 171115067 8032622632 46.94281323572751 56.36869969730791 chr7 159138663 7377410975 46.35838228074092 51.32899175935471 chr8 146364022 7230682548 49.40204873572004 51.548213545634844 chr9 141213431 5388810351 38.16074939075732 57.57036211457713 chr10 135534747 5908877926 43.5967754158275 68.37105674041968 chr11 135006516 6076617566 45.009809496898654 49.93926092982215 chr12 133851895 6208347510 46.38221603063595 49.34336906359302 chr13 115169878 4300819555 37.3432674383835 44.384332484645455 chr14 107349540 4173159449 38.87449772956642 46.92797426718154 chr15 102531392 3840338486 37.455245765121376 46.50785586303813 chr16 90354753 3718437915 41.15376105338919 51.33138033417189 chr17 81195210 3542161710 43.625254617852455 76.27204469593991 chr18 78077248 3607755753 46.207516855614585 67.86460120720413 chr19 59128983 2344945365 39.658137955797415 65.0106517441492 chr20 63025520 2864928087 45.456635454971256 52.272335364643716 chr21 48129895 1727970503 35.90222881225899 64.51793649143903 chr22 51304566 1393582509 27.162933392712063 41.479275297435336 chrMT 16571 19170642 1156.8790054915214 321.0841650184043 chrX 155270560 4296531162 27.671254370435708 36.24750744857351 chrY 59373566 738726882 12.442016401709811 39.42356940975208