BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716378.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 = 1,176,694 number of mapped reads = 1,043,666 (88.69%) number of supplementary alignments = 3,736 (0.32%) number of secondary alignments = 0 number of mapped bases = 59,471,695 bp number of sequenced bases = 59,454,573 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,741 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.655 >>>>>>> ACTG content number of A's = 15,068,061 bp (25.34%) number of C's = 11,458,515 bp (19.27%) number of T's = 17,929,203 bp (30.16%) number of G's = 14,998,370 bp (25.23%) number of N's = 424 bp (0%) GC percentage = 44.5% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 303,239 number of insertions = 3,699 mapped reads with insertion percentage = 0.35% number of deletions = 10,760 mapped reads with deletion percentage = 1.02% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 0.1793X There is a 1.78% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4946938 0.019847244432743057 0.2094949174974391 chr2 243199373 4769023 0.0196095201281625 0.23926597407286532 chr3 198022430 3397493 0.017157111949388765 0.14062126666144723 chr4 191154276 3737870 0.01955420552559337 0.15526786056317046 chr5 180915260 3455076 0.01909775880707907 0.14598254465465882 chr6 171115067 3265159 0.019081656906343614 0.164361479342433 chr7 159138663 3450147 0.021680130616655992 0.2457190364565313 chr8 146364022 3113299 0.0212709309122429 0.1776072184272228 chr9 141213431 1845258 0.013067156480320911 0.13812869141405484 chr10 135534747 2658137 0.019612217965035934 0.22645296008337326 chr11 135006516 2122327 0.015720181979957174 0.1541777679763025 chr12 133851895 2850065 0.021292675759278568 0.15433521333754863 chr13 115169878 1838332 0.015961916708811655 0.13378077616618794 chr14 107349540 2052179 0.019116793607126776 0.14996219455407458 chr15 102531392 2119566 0.02067236149490685 0.15483085761533466 chr16 90354753 1986886 0.021989833783287525 0.16540323243568553 chr17 81195210 2619625 0.032263294842146475 0.19710205139008613 chr18 78077248 1039370 0.01331207267961084 0.1958100931080751 chr19 59128983 1506898 0.025484930123015982 0.2195119179984182 chr20 63025520 1877823 0.029794645089798545 0.18855848269477588 chr21 48129895 725354 0.015070757997706 0.1382928679277907 chr22 51304566 533811 0.010404746431341023 0.1088150924687402 chrMT 16571 70220 4.2375233842254545 3.53343691301873 chrX 155270560 3309146 0.021312127682156876 0.162652355697265 chrY 59373566 181693 0.0030601665394327164 0.09136887441614422