BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781910.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 = 57,331,484 number of mapped reads = 55,856,436 (97.43%) number of supplementary alignments = 213,824 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,172,256 number of mapped paired reads (second in pair) = 27,684,180 number of mapped paired reads (both in pair) = 55,115,418 number of mapped paired reads (singletons) = 741,018 number of mapped bases = 5,542,879,219 bp number of sequenced bases = 5,541,509,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,796,599 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 52,643.0828 std insert size = 2,227,235.4826 median insert size = 272 >>>>>>> Mapping quality mean mapping quality = 53.9705 >>>>>>> ACTG content number of A's = 1,662,743,521 bp (30.01%) number of C's = 1,101,007,139 bp (19.87%) number of T's = 1,660,034,567 bp (29.96%) number of G's = 1,116,751,782 bp (20.15%) number of N's = 972,485 bp (0.02%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 22,570,656 number of insertions = 634,758 mapped reads with insertion percentage = 1.12% number of deletions = 613,959 mapped reads with deletion percentage = 1.08% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 1.7905X std coverageData = 2.5969X There is a 65.21% of reference with a coverageData >= 1X There is a 42.36% of reference with a coverageData >= 2X There is a 26.39% of reference with a coverageData >= 3X There is a 16.24% of reference with a coverageData >= 4X There is a 10.02% of reference with a coverageData >= 5X There is a 6.26% of reference with a coverageData >= 6X There is a 3.97% of reference with a coverageData >= 7X There is a 2.56% of reference with a coverageData >= 8X There is a 1.69% of reference with a coverageData >= 9X There is a 1.13% of reference with a coverageData >= 10X There is a 0.77% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 435654528 1.74785734234941 2.9828142920860965 chr2 243199373 445477459 1.8317376953105877 3.9516040102892047 chr3 198022430 375270890 1.8950928437753238 2.158075990004748 chr4 191154276 355613053 1.8603457921077318 2.26750453127561 chr5 180915260 335010850 1.8517556230469447 2.102422507863293 chr6 171115067 322316625 1.8836250404530421 2.317176513025098 chr7 159138663 279799244 1.7582103476639113 2.2157631141193272 chr8 146364022 268563011 1.8348977250707144 2.1525452785395953 chr9 141213431 217519948 1.5403630268001915 2.363543421043873 chr10 135534747 304156528 2.2441221512000906 3.340110775382268 chr11 135006516 244734641 1.8127616966280353 2.1895401197654563 chr12 133851895 364598172 2.723892493266532 3.1380582977481892 chr13 115169878 170168071 1.4775397348254549 1.9551465771219347 chr14 107349540 161968890 1.5087991061722295 2.033309302003933 chr15 102531392 151353838 1.4761707126730514 2.0806013386654736 chr16 90354753 190025264 2.1031020249703962 2.667023173898438 chr17 81195210 122092557 1.503691621710197 2.133191332444896 chr18 78077248 139381077 1.785168926548231 2.321037908007299 chr19 59128983 80687796 1.364606524688578 2.4025522886676702 chr20 63025520 102981139 1.6339593707437876 2.271778765361184 chr21 48129895 63919967 1.328072022596351 2.657547010729638 chr22 51304566 51073376 0.9954937734002077 1.7620746752380252 chrMT 16571 256307 15.467201737975982 5.54040727212565 chrX 155270560 355146258 2.287273633842758 2.6180347767187366 chrY 59373566 5109730 0.08606068902784111 0.8898731995687699