BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174082.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 = 1,982,874 number of mapped reads = 1,939,197 (97.8%) number of supplementary alignments = 256,605 (12.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 968,113 number of mapped paired reads (second in pair) = 971,084 number of mapped paired reads (both in pair) = 1,912,314 number of mapped paired reads (singletons) = 26,883 number of mapped bases = 217,040,826 bp number of sequenced bases = 216,895,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,484,468 duplication rate = 64.12% >>>>>>> Insert size mean insert size = 909,882.7243 std insert size = 8,917,412.7017 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 52.657 >>>>>>> ACTG content number of A's = 64,974,123 bp (29.96%) number of C's = 42,939,785 bp (19.8%) number of T's = 64,424,318 bp (29.7%) number of G's = 44,555,291 bp (20.54%) number of N's = 1,718 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,821,584 number of insertions = 22,561 mapped reads with insertion percentage = 1.13% number of deletions = 62,469 mapped reads with deletion percentage = 3.15% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0701X std coverageData = 1.4431X There is a 1.68% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% 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 17092462 0.06857540387030771 0.8072735380857963 chr2 243199373 20443872 0.08406219040704517 4.382109298898271 chr3 198022430 15400316 0.07777056366796428 0.7830876850251361 chr4 191154276 15407840 0.08060421311213567 0.8615621455321533 chr5 180915260 12829758 0.07091584203565802 0.7413082931244073 chr6 171115067 12045796 0.07039588162040693 0.7713103242423924 chr7 159138663 12502486 0.07856347266157439 0.8917137053112955 chr8 146364022 10901050 0.07447902736643845 0.9261610792769404 chr9 141213431 8427618 0.059680003101121454 0.7397222905627424 chr10 135534747 10279139 0.07584135601773027 0.9631673620379583 chr11 135006516 9750234 0.07222046971421735 0.7537480672209148 chr12 133851895 10701474 0.07995011202493622 0.799558139224004 chr13 115169878 8106662 0.07038873480442516 0.7368824334133436 chr14 107349540 6735241 0.06274121901221003 0.6993998499882665 chr15 102531392 6082205 0.05932041769217373 0.6798024619040464 chr16 90354753 6708188 0.07424277945843093 0.8073408325740205 chr17 81195210 5864233 0.07222387872388039 0.752817155926889 chr18 78077248 5917061 0.0757847023501648 0.9722431381857817 chr19 59128983 3962614 0.06701644098969198 0.7522572212874791 chr20 63025520 4765035 0.07560485022574982 0.7579689010115493 chr21 48129895 2900034 0.0602543180283273 0.7263775528326895 chr22 51304566 2784553 0.05427495478667532 0.6673996981502726 chrMT 16571 337426 20.362440407941584 22.069925560164013 chrX 155270560 5464185 0.035191378198159394 0.5142490386034196 chrY 59373566 1631344 0.027475930955536677 0.53255786961982