BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472467.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 180,012 number of mapped reads = 178,375 (99.09%) number of supplementary alignments = 722 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 89,459 number of mapped paired reads (second in pair) = 88,916 number of mapped paired reads (both in pair) = 177,374 number of mapped paired reads (singletons) = 1,001 number of mapped bases = 17,493,357 bp number of sequenced bases = 17,491,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,807 duplication rate = 20.27% >>>>>>> Insert size mean insert size = 19,575.754 std insert size = 1,410,835.5739 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.7919 >>>>>>> ACTG content number of A's = 4,780,121 bp (27.33%) number of C's = 3,984,370 bp (22.78%) number of T's = 4,778,742 bp (27.32%) number of G's = 3,945,964 bp (22.56%) number of N's = 2,304 bp (0.01%) GC percentage = 45.34% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 93,823 number of insertions = 1,009 mapped reads with insertion percentage = 0.56% number of deletions = 799 mapped reads with deletion percentage = 0.44% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0057X std coverageData = 0.1972X There is a 0.2% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 1742792 0.006992127012594283 0.21639571210678973 chr2 243199373 1616112 0.006645214500614687 0.2300761092772186 chr3 198022430 1435179 0.007247557764037135 0.1935999948772046 chr4 191154276 530577 0.002775648084377668 0.13872451173028646 chr5 180915260 649294 0.0035889399269027943 0.14002529260093455 chr6 171115067 1230179 0.0071891915865012635 0.19109473598834895 chr7 159138663 1308207 0.008220547887850484 0.29322270537213607 chr8 146364022 1245369 0.008508709879535833 0.2384419695442794 chr9 141213431 721740 0.005110986928715017 0.17814327476119876 chr10 135534747 247938 0.0018293316325738963 0.08390575709918886 chr11 135006516 505322 0.0037429452664343994 0.14866340274986867 chr12 133851895 859940 0.0064245635073003635 0.18185863085063503 chr13 115169878 511317 0.004439676492493983 0.16445883819106305 chr14 107349540 474655 0.004421583921086201 0.21235743683561087 chr15 102531392 269083 0.0026243962434451293 0.0978683686856313 chr16 90354753 1034878 0.011453498190626452 0.30896070834241984 chr17 81195210 698649 0.008604559308363142 0.2353423886090536 chr18 78077248 190601 0.002441184914714207 0.0984601915358895 chr19 59128983 324711 0.005491570859590127 0.16294230208331195 chr20 63025520 720429 0.011430750591189092 0.3731209899106972 chr21 48129895 119207 0.0024767766478609606 0.18771989999637181 chr22 51304566 111223 0.002167896713130757 0.07943907841747944 chrMT 16571 0 0.0 0.0 chrX 155270560 939183 0.006048686885653017 0.1766281323942565 chrY 59373566 6772 1.1405749151061602E-4 0.016789788208622914