BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524824.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,593,775 number of mapped reads = 1,447,774 (90.84%) number of supplementary alignments = 5,362 (0.34%) number of secondary alignments = 0 number of mapped bases = 82,883,915 bp number of sequenced bases = 82,858,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,487 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7419 >>>>>>> ACTG content number of A's = 19,914,590 bp (24.03%) number of C's = 14,795,665 bp (17.86%) number of T's = 25,854,068 bp (31.2%) number of G's = 22,284,689 bp (26.89%) number of N's = 9,962 bp (0.01%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 413,630 number of insertions = 5,045 mapped reads with insertion percentage = 0.35% number of deletions = 15,304 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.59% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 0.2294X There is a 2.38% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 6591379 0.026444784665150343 0.260594359303072 chr2 243199373 7007126 0.028812270005317817 0.35682071506107377 chr3 198022430 5353601 0.027035326250667666 0.1817374293218762 chr4 191154276 5287974 0.02766338326640415 0.21658632208720296 chr5 180915260 4884710 0.0269999888345516 0.18067758653754665 chr6 171115067 4651746 0.027184900088313087 0.19674863947460766 chr7 159138663 4467275 0.028071588109295602 0.26976935811528413 chr8 146364022 4121601 0.028159932636997363 0.20613412165981262 chr9 141213431 3525574 0.024966279588518745 0.2052290066307661 chr10 135534747 4107785 0.030307984416719353 0.2928995427405215 chr11 135006516 3762249 0.027867166055896148 0.21335921943889982 chr12 133851895 3763284 0.02811528368724253 0.1855199242606155 chr13 115169878 2615042 0.02270595441631014 0.16634289240443326 chr14 107349540 2495391 0.023245474549774502 0.17216468052740586 chr15 102531392 2387121 0.023281854985446798 0.16999170005737843 chr16 90354753 2583726 0.02859535236624464 0.21034451688168126 chr17 81195210 2417134 0.029769416200783272 0.1991527860969024 chr18 78077248 2145321 0.027476903386758712 0.30541085459290856 chr19 59128983 1869966 0.03162520146845752 0.25276597068976187 chr20 63025520 1857577 0.02947341013608456 0.20098625137442935 chr21 48129895 1106485 0.02298955773745195 0.18824830197179995 chr22 51304566 1080044 0.02105161556185857 0.16165989177166143 chrMT 16571 11157 0.6732846539134633 0.9222101134497892 chrX 155270560 4498480 0.028971879794856152 0.20091350265123073 chrY 59373566 292167 0.00492082621414385 0.14602063984956332