BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926953.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 13,966,454 number of mapped reads = 13,659,167 (97.8%) number of supplementary alignments = 292,595 (2.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,820,462 number of mapped paired reads (second in pair) = 6,838,705 number of mapped paired reads (both in pair) = 13,470,346 number of mapped paired reads (singletons) = 188,821 number of mapped bases = 1,277,711,020 bp number of sequenced bases = 1,276,781,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 759,728 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 182,298.7936 std insert size = 4,200,473.2368 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.2931 >>>>>>> ACTG content number of A's = 364,049,572 bp (28.51%) number of C's = 257,852,407 bp (20.2%) number of T's = 366,816,934 bp (28.73%) number of G's = 288,008,729 bp (22.56%) number of N's = 53,377 bp (0%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 12,012,357 number of insertions = 210,095 mapped reads with insertion percentage = 1.51% number of deletions = 642,487 mapped reads with deletion percentage = 4.58% homopolymer indels = 52.35% >>>>>>> Coverage mean coverageData = 0.4127X std coverageData = 1.6813X There is a 21.82% of reference with a coverageData >= 1X There is a 9.63% of reference with a coverageData >= 2X There is a 4.32% of reference with a coverageData >= 3X There is a 2.14% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% 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 108398722 0.43489850322178336 2.203056409081302 chr2 243199373 110238741 0.45328546550159077 2.80212184551034 chr3 198022430 86166030 0.43513267663668204 1.060314316410214 chr4 191154276 75850637 0.3968032449349969 1.8188450137563172 chr5 180915260 75770465 0.41881743419543493 1.0259280664674713 chr6 171115067 74500781 0.4353841091036127 1.120895228264423 chr7 159138663 67243346 0.4225456261373768 1.1791202386096524 chr8 146364022 62683957 0.42827435419887544 1.1069996962555062 chr9 141213431 54834705 0.38831083284138884 1.7091244724194317 chr10 135534747 61620087 0.45464420278882434 3.343010813176741 chr11 135006516 61014883 0.4519402826453206 1.4000886229115526 chr12 133851895 58800629 0.439296201223001 1.113217402958201 chr13 115169878 37740511 0.3276942865216893 0.8959596889916662 chr14 107349540 38043691 0.3543908152750352 0.9597374086351873 chr15 102531392 37903646 0.36967844930848104 0.9960014847031489 chr16 90354753 39286135 0.4347987648198208 1.3439821086109927 chr17 81195210 35083917 0.4320934326051992 1.191669682451198 chr18 78077248 32649143 0.41816462332278925 1.8757626302760226 chr19 59128983 24342762 0.4116891711125828 1.552313074220768 chr20 63025520 31534152 0.5003394180643016 1.3246473979840259 chr21 48129895 16349859 0.33970277724478726 1.5180216218361338 chr22 51304566 16031205 0.312471311033018 0.9269539136227576 chrMT 16571 621013 37.47589161788667 29.426493693382508 chrX 155270560 68163950 0.43900112165500016 1.1258757181886225 chrY 59373566 2838053 0.047799941812489415 1.3741974721163501