BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716807.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 = 936,045 number of mapped reads = 846,483 (90.43%) number of supplementary alignments = 4,222 (0.45%) number of secondary alignments = 0 number of mapped bases = 49,221,185 bp number of sequenced bases = 49,208,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,709 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9155 >>>>>>> ACTG content number of A's = 12,609,741 bp (25.63%) number of C's = 9,422,304 bp (19.15%) number of T's = 14,777,523 bp (30.03%) number of G's = 12,398,298 bp (25.2%) number of N's = 340 bp (0%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 237,790 number of insertions = 2,986 mapped reads with insertion percentage = 0.35% number of deletions = 8,171 mapped reads with deletion percentage = 0.96% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.1688X There is a 1.46% 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 6383105 0.025609183938602904 0.2670760825248688 chr2 243199373 3970614 0.016326579920911227 0.20515646845889204 chr3 198022430 3219087 0.016256173606191984 0.1362929779977098 chr4 191154276 2081965 0.010891542912699479 0.12183415586848752 chr5 180915260 3635052 0.02009256709467184 0.15232956423873048 chr6 171115067 1848546 0.010802941157718156 0.11722573509328331 chr7 159138663 3275572 0.020583131328682835 0.2612142927431343 chr8 146364022 2201424 0.015040745464073132 0.15675836311383962 chr9 141213431 1381699 0.009784472979769183 0.12642254118879181 chr10 135534747 2274216 0.016779579040347492 0.1567461240777309 chr11 135006516 2192609 0.01624076426059317 0.15993269008676983 chr12 133851895 1889803 0.014118612216883444 0.12797508033162672 chr13 115169878 1439036 0.012494899056852348 0.12089571819484957 chr14 107349540 1062290 0.009895617624444408 0.108737067226681 chr15 102531392 2229167 0.021741312163205587 0.15811518279213221 chr16 90354753 1475324 0.016328128305546915 0.13957239189236909 chr17 81195210 1945481 0.023960539051503162 0.17256535993925773 chr18 78077248 1345569 0.017233816950105618 0.22195700448321826 chr19 59128983 799900 0.013528052731771151 0.18854770442418475 chr20 63025520 1353385 0.021473603073802486 0.15829632837652213 chr21 48129895 653100 0.013569528875971992 0.12887321715074004 chr22 51304566 582680 0.0113572737366105 0.11382573957436773 chrMT 16571 15403 0.9295154185022027 1.1175076339289773 chrX 155270560 1847619 0.011899351686501292 0.12465695069354656 chrY 59373566 118539 0.0019964945342848366 0.06278681755780609