BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716563.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 = 16,901,262 number of mapped reads = 16,476,162 (97.48%) number of supplementary alignments = 8,589 (0.05%) number of secondary alignments = 0 number of mapped bases = 1,122,258,436 bp number of sequenced bases = 1,122,068,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 860,003 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1889 >>>>>>> ACTG content number of A's = 319,613,692 bp (28.48%) number of C's = 232,233,829 bp (20.7%) number of T's = 338,319,408 bp (30.15%) number of G's = 231,844,683 bp (20.66%) number of N's = 56,762 bp (0.01%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 3,315,356 number of insertions = 99,959 mapped reads with insertion percentage = 0.6% number of deletions = 99,382 mapped reads with deletion percentage = 0.6% homopolymer indels = 38.64% >>>>>>> Coverage mean coverageData = 0.3625X std coverageData = 4.0863X There is a 27.76% of reference with a coverageData >= 1X There is a 5.52% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 96457270 0.38698908597704157 10.420044600740503 chr2 243199373 77812912 0.31995523277932136 2.221338334456207 chr3 198022430 74695395 0.377206738650768 1.2435093535386321 chr4 191154276 61026194 0.31925100121746686 1.3796958639609802 chr5 180915260 64451843 0.3562543203928734 0.7705301420939902 chr6 171115067 67038371 0.39177363031392204 1.5732562693613805 chr7 159138663 53262627 0.33469319143393833 3.7675681558525227 chr8 146364022 96484837 0.6592114351708646 2.6766091635447284 chr9 141213431 46492471 0.3292354747757669 2.086257572553929 chr10 135534747 59516338 0.439122360260871 7.264257770809718 chr11 135006516 53808341 0.39856106648956113 1.8265839047746886 chr12 133851895 44709933 0.33402540173226536 0.8141825712178639 chr13 115169878 29378654 0.2550897379608234 0.6128130460260802 chr14 107349540 25984016 0.24205055745930537 0.9947038487349115 chr15 102531392 32595244 0.3179050178115206 0.6162324480369527 chr16 90354753 38875656 0.4302557940698482 2.882118858289634 chr17 81195210 35988732 0.4432371318455855 1.5930202204927486 chr18 78077248 26778298 0.3429718475733161 4.4763184851427855 chr19 59128983 23528268 0.39791430202680805 7.555179038810428 chr20 63025520 25186368 0.3996217405266946 0.8491452331138065 chr21 48129895 16163929 0.3358396896565014 1.4049248990982326 chr22 51304566 10769457 0.20991225225450694 0.5563343900652902 chrMT 16571 7747827 467.55337638042363 97.37891863135485 chrX 155270560 49915551 0.3214746633231696 1.3432257438910773 chrY 59373566 3589904 0.06046300132958159 2.224039073387027