BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173890.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 = 6,122,824 number of mapped reads = 5,947,930 (97.14%) number of supplementary alignments = 604,392 (9.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,977,306 number of mapped paired reads (second in pair) = 2,970,624 number of mapped paired reads (both in pair) = 5,837,204 number of mapped paired reads (singletons) = 110,726 number of mapped bases = 703,056,724 bp number of sequenced bases = 702,652,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,808,975 duplication rate = 66.18% >>>>>>> Insert size mean insert size = 852,744.4583 std insert size = 8,507,629.1158 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.6263 >>>>>>> ACTG content number of A's = 210,917,535 bp (30.02%) number of C's = 138,388,770 bp (19.7%) number of T's = 210,229,562 bp (29.92%) number of G's = 143,107,187 bp (20.37%) number of N's = 9,028 bp (0%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 7,326,951 number of insertions = 73,512 mapped reads with insertion percentage = 1.19% number of deletions = 163,128 mapped reads with deletion percentage = 2.68% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.2271X std coverageData = 3.1943X There is a 4.19% of reference with a coverageData >= 1X There is a 3.39% of reference with a coverageData >= 2X There is a 2.73% of reference with a coverageData >= 3X There is a 2.31% of reference with a coverageData >= 4X There is a 1.84% of reference with a coverageData >= 5X There is a 1.53% of reference with a coverageData >= 6X There is a 1.19% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% 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 0.03% 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% 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 57014321 0.22874294463643483 2.335322931300899 chr2 243199373 61947641 0.25471957528443134 9.411122651022191 chr3 198022430 67679231 0.34177558067538105 1.8222900141515352 chr4 191154276 29012925 0.15177753596262739 1.5436397401180837 chr5 180915260 29444253 0.16275162747465305 1.2260840752833535 chr6 171115067 48782974 0.28508871167960914 2.029201018429999 chr7 159138663 30587388 0.19220588776719835 1.612570040199788 chr8 146364022 38593548 0.2636819313423896 2.2246898031840896 chr9 141213431 34375403 0.24342870757102417 1.8790752780868472 chr10 135534747 37170132 0.2742479904433658 3.203070970199031 chr11 135006516 30531098 0.22614536619847297 1.4821573619412682 chr12 133851895 27055643 0.20213119134398508 1.383241270403302 chr13 115169878 16376032 0.1421902348459551 1.1455345113451163 chr14 107349540 17190263 0.16013355064213597 1.2182732639673983 chr15 102531392 18264573 0.1781363994355992 1.2831430148112442 chr16 90354753 16894114 0.186975376934515 1.5318546863839728 chr17 81195210 32864790 0.4047626701131754 2.178171439451443 chr18 78077248 19167885 0.24549898326334452 2.269089207897407 chr19 59128983 11033207 0.1865955820684418 1.6101280399578757 chr20 63025520 37338499 0.5924346042682392 2.6229419987819993 chr21 48129895 12421211 0.2580768356132919 1.6345583219072313 chr22 51304566 4833759 0.09421693577916632 0.8841971446239564 chrMT 16571 2438022 147.12582221954017 103.07104201010793 chrX 155270560 20908520 0.13465862427494305 1.1080857005285196 chrY 59373566 1131292 0.019053799126702277 0.7810359739089779