BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063542.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,181,971 number of mapped reads = 1,834,612 (84.08%) number of supplementary alignments = 16,837 (0.77%) number of secondary alignments = 0 number of mapped bases = 116,941,129 bp number of sequenced bases = 116,889,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,050 duplication rate = 8.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7231 >>>>>>> ACTG content number of A's = 30,928,323 bp (26.46%) number of C's = 20,810,137 bp (17.8%) number of T's = 37,901,822 bp (32.43%) number of G's = 27,246,475 bp (23.31%) number of N's = 2,786 bp (0%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 988,999 number of insertions = 8,517 mapped reads with insertion percentage = 0.46% number of deletions = 32,221 mapped reads with deletion percentage = 1.74% homopolymer indels = 45.83% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3988X There is a 2.66% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 9202596 0.036921055454461636 0.6254478200776035 chr2 243199373 8937947 0.03675152155922705 0.562255923549394 chr3 198022430 9541967 0.048186293845601226 0.29655254762236366 chr4 191154276 9468811 0.04953491597540826 0.3087706631923973 chr5 180915260 4482284 0.024775599360717278 0.21531911906437232 chr6 171115067 9101980 0.053192159869826075 0.37073173417502764 chr7 159138663 4610799 0.028973468251395327 0.41640402752924843 chr8 146364022 3130828 0.021390693950730597 0.5197530502160179 chr9 141213431 4398046 0.031144672067347477 0.37109783948237884 chr10 135534747 2220531 0.01638348135183371 0.2294280157386306 chr11 135006516 6831525 0.05060144652573658 0.44639975520658776 chr12 133851895 5874957 0.0438914742297821 0.30126196527124244 chr13 115169878 1627139 0.014128164657776228 0.16375402882091786 chr14 107349540 3444767 0.03208925720594611 0.29271026652676485 chr15 102531392 2391125 0.02332090644004911 0.2168137908705892 chr16 90354753 2709065 0.029982540044130274 0.25061739121922616 chr17 81195210 2318205 0.028551006888214218 0.26199534856608303 chr18 78077248 2922482 0.037430648170386334 0.5937547389779392 chr19 59128983 3351594 0.05668276080446031 0.450188014850915 chr20 63025520 1831579 0.02906091056448245 0.24559216733646747 chr21 48129895 1853632 0.03851311123782838 0.27350488743471224 chr22 51304566 1358475 0.026478637398472487 0.21372055812375051 chrMT 16571 113080 6.823969585420312 5.653449579093024 chrX 155270560 14897148 0.0959431588319125 0.48563080782050866 chrY 59373566 320567 0.005399153555978093 0.13415692610932026