BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173886.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,761,680 number of mapped reads = 4,630,995 (97.26%) number of supplementary alignments = 464,835 (9.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,319,281 number of mapped paired reads (second in pair) = 2,311,714 number of mapped paired reads (both in pair) = 4,543,690 number of mapped paired reads (singletons) = 87,305 number of mapped bases = 543,145,517 bp number of sequenced bases = 542,835,769 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,502,968 duplication rate = 63.89% >>>>>>> Insert size mean insert size = 935,632.5174 std insert size = 8,533,611.6646 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.688 >>>>>>> ACTG content number of A's = 164,492,357 bp (30.3%) number of C's = 105,039,511 bp (19.35%) number of T's = 164,208,404 bp (30.25%) number of G's = 109,089,620 bp (20.1%) number of N's = 5,877 bp (0%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 5,515,035 number of insertions = 56,741 mapped reads with insertion percentage = 1.18% number of deletions = 125,824 mapped reads with deletion percentage = 2.64% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.1755X std coverageData = 2.6534X There is a 3.93% of reference with a coverageData >= 1X There is a 3.04% of reference with a coverageData >= 2X There is a 2.28% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 1.36% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.64% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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% 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 48799181 0.19578358843888297 1.5317234767455656 chr2 243199373 40793362 0.16773629593198006 7.784335572828668 chr3 198022430 34040992 0.17190472816640015 1.154149304990835 chr4 191154276 34230751 0.179073948625664 1.4102477786656091 chr5 180915260 26833144 0.14831885381034193 1.0647189439663873 chr6 171115067 26269264 0.15351812356769262 1.1256940953081447 chr7 159138663 48729125 0.30620544424204443 3.0033595735912266 chr8 146364022 53579341 0.3660690671646069 2.0744576328624986 chr9 141213431 18983620 0.13443211361389554 1.3105151646704276 chr10 135534747 24741437 0.1825468195251805 3.046560392356883 chr11 135006516 22270470 0.16495848244835826 1.1738524785653375 chr12 133851895 20867756 0.15590183463596088 1.1065505865879972 chr13 115169878 14121567 0.12261510774544712 0.9795093244516848 chr14 107349540 18079478 0.1684169117073068 1.1538646856983334 chr15 102531392 13065185 0.12742619353105047 0.979717197110467 chr16 90354753 12265843 0.13575205058664705 1.2604640213164204 chr17 81195210 13097000 0.1613026187135916 1.2011740061818894 chr18 78077248 10263168 0.13144889532991735 1.6162920387898094 chr19 59128983 6817487 0.11529856686356334 1.182187076791819 chr20 63025520 20469478 0.3247807872112757 1.6027777661769802 chr21 48129895 6388234 0.1327290242374308 1.0847515173271014 chr22 51304566 5340797 0.10409983781950324 0.8582084891455158 chrMT 16571 1164253 70.25846358095468 54.956715128090714 chrX 155270560 20920821 0.13473784727768098 1.018023336042343 chrY 59373566 1013763 0.01707431552957422 0.7160199201527088