BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173988.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 = 10,664,012 number of mapped reads = 10,439,499 (97.89%) number of supplementary alignments = 1,422,973 (13.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,221,154 number of mapped paired reads (second in pair) = 5,218,345 number of mapped paired reads (both in pair) = 10,292,716 number of mapped paired reads (singletons) = 146,783 number of mapped bases = 1,184,706,827 bp number of sequenced bases = 1,183,897,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,412,499 duplication rate = 64.59% >>>>>>> Insert size mean insert size = 1,084,367.2932 std insert size = 9,594,124.826 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 52.5759 >>>>>>> ACTG content number of A's = 353,331,151 bp (29.84%) number of C's = 235,536,906 bp (19.9%) number of T's = 350,471,938 bp (29.6%) number of G's = 244,548,482 bp (20.66%) number of N's = 9,326 bp (0%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 9,806,942 number of insertions = 131,223 mapped reads with insertion percentage = 1.21% number of deletions = 333,138 mapped reads with deletion percentage = 3.11% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.3827X std coverageData = 6.4255X There is a 8.02% of reference with a coverageData >= 1X There is a 6% of reference with a coverageData >= 2X There is a 4.48% of reference with a coverageData >= 3X There is a 3.62% of reference with a coverageData >= 4X There is a 2.75% of reference with a coverageData >= 5X There is a 2.29% of reference with a coverageData >= 6X There is a 1.74% of reference with a coverageData >= 7X There is a 1.51% of reference with a coverageData >= 8X There is a 1.15% of reference with a coverageData >= 9X There is a 1.03% of reference with a coverageData >= 10X There is a 0.79% of reference with a coverageData >= 11X There is a 0.72% of reference with a coverageData >= 12X There is a 0.54% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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% 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 97570963 0.39145725137431053 2.8917957892283317 chr2 243199373 105834216 0.4351747074611085 21.22223309597487 chr3 198022430 81535512 0.4117488710748575 1.9728422157712395 chr4 191154276 77787774 0.4069371380423632 2.8360377403682775 chr5 180915260 72264969 0.39944098137437384 1.9233796011635804 chr6 171115067 73505214 0.4295659949103138 2.3317531871895163 chr7 159138663 66400187 0.41724735993289075 2.7722365296127798 chr8 146364022 60791474 0.4153443801920119 3.5498006193328844 chr9 141213431 48736639 0.3451275041961129 2.609904200753651 chr10 135534747 57724211 0.42589972149355915 3.753775901343692 chr11 135006516 55301759 0.40962288812785896 2.0547082033967192 chr12 133851895 54693752 0.4086139535043564 2.06865199843242 chr13 115169878 40007974 0.34738227299329083 1.8148445452463873 chr14 107349540 35410820 0.3298646645341936 1.782247998315523 chr15 102531392 34733829 0.33876287371578845 1.8699405751189708 chr16 90354753 36351931 0.40232450195508807 2.6326023684410487 chr17 81195210 33042251 0.4069482793381531 2.1389260947640465 chr18 78077248 32375254 0.41465669999024557 3.549894618015595 chr19 59128983 23014122 0.3892189723608133 2.4855341191732765 chr20 63025520 25822680 0.4097178412808018 2.0810840885242956 chr21 48129895 16496968 0.3427592767447342 2.5740499500735012 chr22 51304566 15149716 0.2952898188438043 2.219047957334707 chrMT 16571 1969140 118.83048699535333 98.28126166665737 chrX 155270560 29797934 0.19190974773324704 1.3468864282855355 chrY 59373566 8387538 0.1412672097209051 2.041200361692784