BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716661.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 = 2,389,923 number of mapped reads = 2,228,504 (93.25%) number of supplementary alignments = 41,806 (1.75%) number of secondary alignments = 0 number of mapped bases = 177,036,109 bp number of sequenced bases = 176,954,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,976 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.726 >>>>>>> ACTG content number of A's = 47,197,693 bp (26.67%) number of C's = 34,531,744 bp (19.51%) number of T's = 52,628,444 bp (29.74%) number of G's = 42,584,905 bp (24.07%) number of N's = 11,940 bp (0.01%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,153,484 number of insertions = 15,468 mapped reads with insertion percentage = 0.68% number of deletions = 42,247 mapped reads with deletion percentage = 1.87% homopolymer indels = 41.79% >>>>>>> Coverage mean coverageData = 0.0572X std coverageData = 0.47X There is a 4.76% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14613842 0.058631115707430875 0.8693700611188027 chr2 243199373 15045182 0.061863572320969756 0.5544646942831372 chr3 198022430 11613488 0.058647336061879454 0.27729816682567865 chr4 191154276 11379003 0.059527849641197665 0.35683758092996026 chr5 180915260 10694827 0.05911511831561362 0.2840774384003057 chr6 171115067 9932871 0.058047904104201416 0.31042340524940637 chr7 159138663 9969798 0.06264849667613458 0.6482085073703732 chr8 146364022 9094403 0.06213550895724907 0.5944731680547768 chr9 141213431 7407178 0.052453778281189134 0.42082117249089823 chr10 135534747 8433856 0.06222652262006288 0.482957783563744 chr11 135006516 8184098 0.060620022221742245 0.4631793193572328 chr12 133851895 7948900 0.0593857860585388 0.2845118935433748 chr13 115169878 5545379 0.04814956042586066 0.25229105959352477 chr14 107349540 5290479 0.04928273563165711 0.2817223005805847 chr15 102531392 5147084 0.050200079210862565 0.26048411441044467 chr16 90354753 5125730 0.0567289470649098 0.30162295593489624 chr17 81195210 4693273 0.05780233833990946 0.3259023251675672 chr18 78077248 4685986 0.060017304913205956 0.6968463601610105 chr19 59128983 3446432 0.05828667812534506 0.5770507400036404 chr20 63025520 3894926 0.06179918864612303 0.30434488423573036 chr21 48129895 2382528 0.04950204026000888 0.2991375515999428 chr22 51304566 2044633 0.039852846625775956 0.23144918451678692 chrMT 16571 22847 1.3787339327741235 1.4705610064985337 chrX 155270560 9927022 0.06393370385216618 0.3542656730650865 chrY 59373566 512344 0.008629159986786039 0.2920011692395112