BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779307.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 = 14,144,314 number of mapped reads = 13,455,743 (95.13%) number of supplementary alignments = 35,377 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,802,386 number of mapped paired reads (second in pair) = 6,653,357 number of mapped paired reads (both in pair) = 13,281,866 number of mapped paired reads (singletons) = 173,877 number of mapped bases = 1,071,077,758 bp number of sequenced bases = 1,070,872,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 461,708 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 37,663.348 std insert size = 1,812,516.7176 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 52.9712 >>>>>>> ACTG content number of A's = 330,754,335 bp (30.89%) number of C's = 203,249,412 bp (18.98%) number of T's = 329,693,541 bp (30.79%) number of G's = 206,891,845 bp (19.32%) number of N's = 283,499 bp (0.03%) GC percentage = 38.3% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,721,292 number of insertions = 76,979 mapped reads with insertion percentage = 0.57% number of deletions = 99,552 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.346X std coverageData = 1.4604X There is a 14.27% of reference with a coverageData >= 1X There is a 6.79% of reference with a coverageData >= 2X There is a 3.86% of reference with a coverageData >= 3X There is a 2.45% of reference with a coverageData >= 4X There is a 1.66% of reference with a coverageData >= 5X There is a 1.17% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.5% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 69813298 0.28009277457326776 1.680945232163376 chr2 243199373 98882324 0.40658955152816123 1.429025049691064 chr3 198022430 72446702 0.3658509897085901 1.2152035719060936 chr4 191154276 96287000 0.5037135554320532 1.6306291714755339 chr5 180915260 52210024 0.28858828160764327 1.1569503255926898 chr6 171115067 73773356 0.4311330223188353 1.7345339585758146 chr7 159138663 86921643 0.5462006614948123 2.07775918247378 chr8 146364022 83765838 0.5723116709651501 1.6601442564961906 chr9 141213431 44646178 0.31616098896428624 1.306086771628008 chr10 135534747 21531494 0.15886327658840135 1.4248955397719019 chr11 135006516 37977785 0.28130334835097887 1.197061601680533 chr12 133851895 41159781 0.3075024152627798 1.1655727221019885 chr13 115169878 40074385 0.3479589081443674 1.3597637868412402 chr14 107349540 29387596 0.27375614278365795 1.1899265942353583 chr15 102531392 23096917 0.2252667846350901 1.1112484466892274 chr16 90354753 21097217 0.2334931622246812 1.3150041839633342 chr17 81195210 12890391 0.15875802279469442 0.7340381416777865 chr18 78077248 25946200 0.3323144791168869 1.2492488793652092 chr19 59128983 7624131 0.128940675336831 1.0149721079111196 chr20 63025520 20386946 0.3234712859171967 1.2027490435252517 chr21 48129895 11912777 0.24751304776376512 0.9479558766650363 chr22 51304566 4446350 0.08666577551791395 0.5146255202214296 chrMT 16571 1043 0.0629412829642146 0.3233400648915518 chrX 155270560 94033852 0.6056128863063288 2.2410891527501478 chrY 59373566 764530 0.0128766057272019 0.18762727774685656