BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264619.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,787,448,744 number of mapped reads = 1,776,555,689 (99.39%) number of supplementary alignments = 10,961,879 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 891,852,927 number of mapped paired reads (second in pair) = 884,702,762 number of mapped paired reads (both in pair) = 1,767,997,958 number of mapped paired reads (singletons) = 8,557,731 number of mapped bases = 178,329,526,981 bp number of sequenced bases = 178,287,889,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 724,983,196 duplication rate = 40.44% >>>>>>> Insert size mean insert size = 74,181.4162 std insert size = 2,615,784.7981 median insert size = 339 >>>>>>> Mapping quality mean mapping quality = 54.5315 >>>>>>> ACTG content number of A's = 55,184,942,129 bp (30.95%) number of C's = 33,816,907,324 bp (18.97%) number of T's = 55,053,901,857 bp (30.88%) number of G's = 34,220,771,845 bp (19.19%) number of N's = 11,366,729 bp (0.01%) GC percentage = 38.16% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 798,935,624 number of insertions = 19,751,427 mapped reads with insertion percentage = 1.1% number of deletions = 18,718,770 mapped reads with deletion percentage = 1.03% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 57.6057X std coverageData = 58.0608X There is a 90.93% of reference with a coverageData >= 1X There is a 89.84% of reference with a coverageData >= 2X There is a 88.78% of reference with a coverageData >= 3X There is a 87.74% of reference with a coverageData >= 4X There is a 86.69% of reference with a coverageData >= 5X There is a 85.64% of reference with a coverageData >= 6X There is a 84.59% of reference with a coverageData >= 7X There is a 83.54% of reference with a coverageData >= 8X There is a 82.5% of reference with a coverageData >= 9X There is a 81.45% of reference with a coverageData >= 10X There is a 80.41% of reference with a coverageData >= 11X There is a 79.38% of reference with a coverageData >= 12X There is a 78.35% of reference with a coverageData >= 13X There is a 77.32% of reference with a coverageData >= 14X There is a 76.29% of reference with a coverageData >= 15X There is a 75.27% of reference with a coverageData >= 16X There is a 74.26% of reference with a coverageData >= 17X There is a 73.26% of reference with a coverageData >= 18X There is a 72.26% of reference with a coverageData >= 19X There is a 71.26% of reference with a coverageData >= 20X There is a 70.27% of reference with a coverageData >= 21X There is a 69.28% of reference with a coverageData >= 22X There is a 68.31% of reference with a coverageData >= 23X There is a 67.33% of reference with a coverageData >= 24X There is a 66.37% of reference with a coverageData >= 25X There is a 65.41% of reference with a coverageData >= 26X There is a 64.46% of reference with a coverageData >= 27X There is a 63.52% of reference with a coverageData >= 28X There is a 62.58% of reference with a coverageData >= 29X There is a 61.65% of reference with a coverageData >= 30X There is a 60.73% of reference with a coverageData >= 31X There is a 59.81% of reference with a coverageData >= 32X There is a 58.9% of reference with a coverageData >= 33X There is a 58% of reference with a coverageData >= 34X There is a 57.11% of reference with a coverageData >= 35X There is a 56.23% of reference with a coverageData >= 36X There is a 55.35% of reference with a coverageData >= 37X There is a 54.48% of reference with a coverageData >= 38X There is a 53.62% of reference with a coverageData >= 39X There is a 52.77% of reference with a coverageData >= 40X There is a 51.93% of reference with a coverageData >= 41X There is a 51.1% of reference with a coverageData >= 42X There is a 50.27% of reference with a coverageData >= 43X There is a 49.46% of reference with a coverageData >= 44X There is a 48.65% of reference with a coverageData >= 45X There is a 47.85% of reference with a coverageData >= 46X There is a 47.07% of reference with a coverageData >= 47X There is a 46.29% of reference with a coverageData >= 48X There is a 45.52% of reference with a coverageData >= 49X There is a 44.76% of reference with a coverageData >= 50X There is a 44.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14036404336 56.314420721142355 59.82961496622681 chr2 243199373 16346097212 67.21274405588208 59.82005620417418 chr3 198022430 13261829503 66.97135017987608 55.8256144172626 chr4 191154276 14933027841 78.12029191018463 62.632006039734634 chr5 180915260 13237095615 73.16738021436113 59.09449100195051 chr6 171115067 12203429241 71.31709354968724 60.467424185736895 chr7 159138663 10022030625 62.9767175120731 60.04633184369701 chr8 146364022 10157024267 69.39563513087937 57.986510647443836 chr9 141213431 7765401478 54.99053045457128 62.85286505193224 chr10 135534747 7464113397 55.07158542155983 51.14713278476191 chr11 135006516 8617022257 63.82671379357719 59.92332377008245 chr12 133851895 8896563092 66.46572386591912 63.206995748901036 chr13 115169878 7217539799 62.66864152621574 60.54017883278564 chr14 107349540 5069954880 47.228473265931086 53.11017774381952 chr15 102531392 4539811545 44.27728382932712 54.05584939274286 chr16 90354753 3251061488 35.981078803900886 44.46173651993646 chr17 81195210 2717026919 33.46289662900065 42.79462104877803 chr18 78077248 4828817199 61.84666241053988 52.982583068830515 chr19 59128983 1332154377 22.529634527960678 32.90922584526964 chr20 63025520 2673201613 42.41459035958767 56.15037722789811 chr21 48129895 2011840857 41.80023365935039 59.5851596425713 chr22 51304566 903343664 17.607471116703337 29.2932268016362 chrMT 16571 105783 6.383621990223885 8.992207912431843 chrX 155270560 6094589096 39.25141440850088 39.47097198569233 chrY 59373566 750040897 12.632572835527514 27.225837004594432