BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971278.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,180,827 number of mapped reads = 8,953,822 (73.51%) number of secondary alignments = 0 number of mapped bases = 353,987,930 bp number of sequenced bases = 353,953,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 845,708 duplication rate = 8.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2368 >>>>>>> ACTG content number of A's = 101,741,595 bp (28.74%) number of C's = 73,462,014 bp (20.75%) number of T's = 103,434,987 bp (29.22%) number of G's = 75,311,879 bp (21.28%) number of N's = 2,991 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 861,231 number of insertions = 10,719 mapped reads with insertion percentage = 0.12% number of deletions = 26,674 mapped reads with deletion percentage = 0.3% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.1143X std coverageData = 0.9579X There is a 6.28% of reference with a coverageData >= 1X There is a 2.66% of reference with a coverageData >= 2X There is a 1.23% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 29810757 0.11960153551633478 1.3925184182983807 chr2 243199373 30114542 0.1238265610166684 0.6334180012112717 chr3 198022430 24931354 0.12590166679602913 0.5777029342769427 chr4 191154276 21470946 0.1123226037590705 0.5637834562573409 chr5 180915260 22020122 0.1217151167900375 0.5729048526858905 chr6 171115067 20731110 0.12115303674573555 0.5933722125036379 chr7 159138663 18665031 0.11728784600886084 0.9878605794788209 chr8 146364022 18067472 0.12344203003658918 2.9149948307296216 chr9 141213431 15208960 0.10770193665218714 0.6109808248814568 chr10 135534747 17293153 0.12759202627205257 0.699276968466767 chr11 135006516 16747804 0.12405181983956982 0.6870330043572449 chr12 133851895 15991018 0.1194679985666247 0.573933205102141 chr13 115169878 12915969 0.1121471102018533 0.5509018965000552 chr14 107349540 10874101 0.10129620490222874 0.5508574388230226 chr15 102531392 11206432 0.10929757005542264 0.5301724804068645 chr16 90354753 9777743 0.10821503767488579 0.5508809636811254 chr17 81195210 9729680 0.11983071415173382 0.5819344024880735 chr18 78077248 8527672 0.10922096024695953 0.8748907766630291 chr19 59128983 6295360 0.10646826108948973 1.1371475501078656 chr20 63025520 8089505 0.12835284817959455 0.597349234415178 chr21 48129895 4395415 0.09132400974487893 0.5274853516450801 chr22 51304566 4233972 0.08252622193510029 0.48021214315601796 chrMT 16571 43890 2.6486029811115803 3.7522017720760266 chrX 155270560 15955261 0.10275779903157431 0.5487959269123759 chrY 59373566 890661 0.015000968612867214 0.2647132001915755