BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173906.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,562,038 number of mapped reads = 10,275,675 (97.29%) number of supplementary alignments = 1,007,400 (9.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,142,952 number of mapped paired reads (second in pair) = 5,132,723 number of mapped paired reads (both in pair) = 10,082,962 number of mapped paired reads (singletons) = 192,713 number of mapped bases = 1,213,982,822 bp number of sequenced bases = 1,213,359,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,009,016 duplication rate = 65.21% >>>>>>> Insert size mean insert size = 832,273.0608 std insert size = 8,654,244.7125 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.7809 >>>>>>> ACTG content number of A's = 361,633,252 bp (29.8%) number of C's = 241,373,534 bp (19.89%) number of T's = 360,964,135 bp (29.75%) number of G's = 249,373,876 bp (20.55%) number of N's = 14,753 bp (0%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 12,404,337 number of insertions = 123,902 mapped reads with insertion percentage = 1.17% number of deletions = 250,362 mapped reads with deletion percentage = 2.38% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.3922X std coverageData = 5.2885X There is a 7.77% of reference with a coverageData >= 1X There is a 6.24% of reference with a coverageData >= 2X There is a 4.91% of reference with a coverageData >= 3X There is a 4.07% of reference with a coverageData >= 4X There is a 3.15% of reference with a coverageData >= 5X There is a 2.56% of reference with a coverageData >= 6X There is a 1.93% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.98% of reference with a coverageData >= 10X There is a 0.74% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.48% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 97094844 0.38954704951367003 3.3620699668556933 chr2 243199373 105767751 0.4349014131709953 16.818832149087207 chr3 198022430 91571024 0.46242753409298126 2.03304540953703 chr4 191154276 54357733 0.28436577060928525 1.967038092823104 chr5 180915260 72505706 0.40077164303331847 1.8256016728459583 chr6 171115067 63875589 0.3732902667185935 2.1764643810946356 chr7 159138663 66165241 0.4157709996595862 2.8487662029389202 chr8 146364022 68330678 0.4668543339154755 2.9375577226277336 chr9 141213431 49352482 0.34948858370277824 2.2308888972594425 chr10 135534747 57577256 0.42481546079102506 4.0046487199352 chr11 135006516 46223604 0.3423805410992163 1.7566916125269023 chr12 133851895 56329591 0.4208352149216864 1.9042439220249574 chr13 115169878 29882228 0.25946218333234666 1.4720466093004272 chr14 107349540 38985177 0.36316109971221117 1.7663550356022526 chr15 102531392 46275690 0.4513319198865456 1.9684740041318805 chr16 90354753 42862847 0.4743839762364244 2.654949002556091 chr17 81195210 55835272 0.6876670680450239 2.9519681066378998 chr18 78077248 22428462 0.2872598942011891 3.2727969939264585 chr19 59128983 21390158 0.36175420098126837 2.4505790631394366 chr20 63025520 59956801 0.9513098979587951 3.4951896207791364 chr21 48129895 13491341 0.28031104160937814 1.683215888425385 chr22 51304566 10162189 0.1980757229288325 1.2307159528687555 chrMT 16571 2728602 164.66127572264799 127.0421980115393 chrX 155270560 39001410 0.25118354696473044 1.4428304384604742 chrY 59373566 1831146 0.03084109854543687 1.1208902604842172