BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819083.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,354,064 number of mapped reads = 1,242,607 (91.77%) number of supplementary alignments = 5,266 (0.39%) number of secondary alignments = 0 number of mapped bases = 73,035,071 bp number of sequenced bases = 73,013,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,671 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2112 >>>>>>> ACTG content number of A's = 18,212,864 bp (24.94%) number of C's = 13,902,777 bp (19.04%) number of T's = 23,156,668 bp (31.72%) number of G's = 17,740,026 bp (24.3%) number of N's = 972 bp (0%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 369,696 number of insertions = 4,731 mapped reads with insertion percentage = 0.38% number of deletions = 13,015 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.0236X std coverageData = 0.2486X There is a 2.13% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7342030 0.029456416078497954 0.4768092661194268 chr2 243199373 4927750 0.02026218217264894 0.25725664199389126 chr3 198022430 2186353 0.01104093612021628 0.11706928492905525 chr4 191154276 4093363 0.021413923275250196 0.1727898715271464 chr5 180915260 4229929 0.023380719791133153 0.16518806623798601 chr6 171115067 3394657 0.019838445903773046 0.1899811354913087 chr7 159138663 3921640 0.024642911572029483 0.3164983178751241 chr8 146364022 6712738 0.04586330648935023 0.27378638715050535 chr9 141213431 2618605 0.01854359731547065 0.19248055988027646 chr10 135534747 3905337 0.02881428627302488 0.2497196017902734 chr11 135006516 3015779 0.022338025521671856 0.25856645937037115 chr12 133851895 3704597 0.027676836401905255 0.17962460789624607 chr13 115169878 1745815 0.01515860770469862 0.13323098539704842 chr14 107349540 1869362 0.0174137867754254 0.14728802199826602 chr15 102531392 2100751 0.020488856720096028 0.15517256384092187 chr16 90354753 2342401 0.025924491210772276 0.18783159199056554 chr17 81195210 2864335 0.03527714258020886 0.21926505720325906 chr18 78077248 1644242 0.021059169503515288 0.40494767943761245 chr19 59128983 1527246 0.025829059160378254 0.30685466292043156 chr20 63025520 2215623 0.03515437873420164 0.20413493127834234 chr21 48129895 1055197 0.021923941450526747 0.17382419389864912 chr22 51304566 673671 0.01313081958436214 0.12331932076898906 chrMT 16571 8575 0.5174702794037777 0.7557113557810603 chrX 155270560 4687080 0.03018653375115025 0.20871612278037927 chrY 59373566 247995 0.0041768587724712375 0.12640229512005444