BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124927.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,357,310 number of mapped reads = 2,331,811 (98.92%) number of supplementary alignments = 40,934 (1.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,166,971 number of mapped paired reads (second in pair) = 1,164,840 number of mapped paired reads (both in pair) = 2,325,620 number of mapped paired reads (singletons) = 6,191 number of mapped bases = 310,162,016 bp number of sequenced bases = 309,895,396 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 390,214 duplication rate = 15.67% >>>>>>> Insert size mean insert size = 109,323.6759 std insert size = 3,228,217.9737 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.3136 >>>>>>> ACTG content number of A's = 90,509,944 bp (29.21%) number of C's = 62,539,717 bp (20.18%) number of T's = 90,303,097 bp (29.14%) number of G's = 66,515,876 bp (21.46%) number of N's = 26,762 bp (0.01%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 3,275,081 number of insertions = 68,090 mapped reads with insertion percentage = 2.7% number of deletions = 127,490 mapped reads with deletion percentage = 5.21% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.1002X std coverageData = 1.2022X There is a 5.51% of reference with a coverageData >= 1X There is a 3.07% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% 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 21835972 0.08760648985504434 1.2572965192311503 chr2 243199373 24877718 0.10229351208072399 2.2305853753781815 chr3 198022430 26172521 0.1321694769627865 0.5263681760049711 chr4 191154276 15707056 0.08216952468277508 0.8293960978900558 chr5 180915260 17230228 0.09523921862644423 0.4645638591240114 chr6 171115067 21223802 0.12403233901080142 0.9752711858401028 chr7 159138663 22366465 0.14054702093356156 1.3062587279178435 chr8 146364022 22638096 0.15466981359667747 0.747418267399351 chr9 141213431 10733177 0.07600677162216957 1.8342658248442159 chr10 135534747 14968054 0.11043702320852083 1.965953787204101 chr11 135006516 18186167 0.13470584634596453 0.870436912486023 chr12 133851895 13364266 0.09984368170506663 0.4535043020196167 chr13 115169878 6149385 0.05339403936852308 0.32744999931532714 chr14 107349540 9483578 0.08834297752929356 0.4671035337262488 chr15 102531392 5892879 0.05747390028607043 0.33825024650783014 chr16 90354753 9201155 0.10183365782650083 1.5767753922102485 chr17 81195210 8873313 0.1092837003562156 1.1884280994309666 chr18 78077248 5093301 0.06523412556754049 1.82061223263295 chr19 59128983 4677082 0.07909965236506773 0.8317343021785395 chr20 63025520 7853634 0.1246103800492245 0.5421514157179487 chr21 48129895 4660762 0.09683715287556725 0.666992706531618 chr22 51304566 2913118 0.05678087209625748 0.37644278073268234 chrMT 16571 394091 23.781968499185325 13.367276015066121 chrX 155270560 11020846 0.0709783361379002 0.5132288114314023 chrY 59373566 4645350 0.07823936328836978 1.8838772932259127