BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124924.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,839,230 number of mapped reads = 3,792,609 (98.79%) number of supplementary alignments = 20,194 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,899,686 number of mapped paired reads (second in pair) = 1,892,923 number of mapped paired reads (both in pair) = 3,777,576 number of mapped paired reads (singletons) = 15,033 number of mapped bases = 329,534,755 bp number of sequenced bases = 329,353,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,747 duplication rate = 4.95% >>>>>>> Insert size mean insert size = 51,294.9552 std insert size = 2,117,715.2854 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 52.9004 >>>>>>> ACTG content number of A's = 92,611,511 bp (28.12%) number of C's = 61,451,898 bp (18.66%) number of T's = 98,172,106 bp (29.81%) number of G's = 77,112,882 bp (23.41%) number of N's = 4,748 bp (0%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,425,751 number of insertions = 44,332 mapped reads with insertion percentage = 1.14% number of deletions = 107,185 mapped reads with deletion percentage = 2.77% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.1064X std coverageData = 0.8934X There is a 7.87% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 25122723 0.10079302069221324 0.8603863900626944 chr2 243199373 27194389 0.1118193220012948 1.1980283720922484 chr3 198022430 31354356 0.15833739642524333 0.4990447679754517 chr4 191154276 18656106 0.09759711574539928 0.6326517602614583 chr5 180915260 16985199 0.09388483315337799 0.38527727297269443 chr6 171115067 15970522 0.09333206175234118 0.6371810743799495 chr7 159138663 22174582 0.13934126114908985 1.6327104189545358 chr8 146364022 21191807 0.14478836199240275 0.5980086080048036 chr9 141213431 13268754 0.09396240786756326 1.0621699635655084 chr10 135534747 16150574 0.11916187071939567 1.7350988970361434 chr11 135006516 15138766 0.11213359509255094 0.741915707869312 chr12 133851895 18188242 0.1358833358317415 0.4627439835285875 chr13 115169878 6934812 0.06021376526942227 0.2986053626216163 chr14 107349540 9481713 0.08832560437613426 0.4079917262790409 chr15 102531392 9489265 0.09254985048871667 0.38226190157539386 chr16 90354753 10418927 0.1153113328747631 1.5101277581061874 chr17 81195210 7813709 0.09623362018523014 0.9093686147590191 chr18 78077248 8857793 0.11344909339017686 1.112459203763785 chr19 59128983 3259926 0.055132455093976504 0.6133034814147816 chr20 63025520 10117764 0.1605343993988467 0.5253431080931406 chr21 48129895 3971599 0.0825183391736051 0.4509129498064359 chr22 51304566 3355971 0.06541271589745053 0.3366569071021503 chrMT 16571 199062 12.012672741536418 7.9063022568275585 chrX 155270560 11215838 0.07223415694514143 0.4609425981101707 chrY 59373566 3022356 0.05090406730833718 1.0159298583338472