BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084854.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,235,072 number of mapped reads = 1,771,882 (79.28%) number of supplementary alignments = 15,410 (0.69%) number of secondary alignments = 0 number of mapped bases = 118,637,276 bp number of sequenced bases = 118,595,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,158 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8252 >>>>>>> ACTG content number of A's = 32,369,492 bp (27.29%) number of C's = 22,394,265 bp (18.88%) number of T's = 37,115,431 bp (31.3%) number of G's = 26,698,564 bp (22.51%) number of N's = 17,442 bp (0.01%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,010,028 number of insertions = 8,862 mapped reads with insertion percentage = 0.5% number of deletions = 23,837 mapped reads with deletion percentage = 1.33% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.2895X There is a 3.15% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10070873 0.040404605451314 0.46504380388454797 chr2 243199373 9502709 0.03907373971724837 0.2954553890074063 chr3 198022430 8251006 0.041667027316046976 0.23950285548734243 chr4 191154276 7858369 0.04111008743534463 0.2474133715886137 chr5 180915260 7310247 0.04040702260273677 0.23691272174613962 chr6 171115067 7054240 0.04122512484537671 0.24881138231271988 chr7 159138663 6224527 0.03911385757966309 0.2757800871086006 chr8 146364022 5994606 0.04095682749138992 0.38741302448037224 chr9 141213431 5081637 0.03598550763914234 0.27224238535297446 chr10 135534747 5530584 0.040805654065964356 0.3056971403966761 chr11 135006516 5323696 0.039432881891419226 0.2634675726383412 chr12 133851895 5530580 0.04131865297835342 0.24034299704525428 chr13 115169878 3802065 0.03301266846874666 0.21370573791716554 chr14 107349540 3424371 0.03189926104946514 0.21629298034949204 chr15 102531392 3428703 0.03344051936796098 0.21487419925834425 chr16 90354753 3342849 0.03699693584464782 0.23591105953880107 chr17 81195210 2993049 0.036862383877078464 0.23586432057923135 chr18 78077248 3064256 0.03924646524426681 0.4435942516776322 chr19 59128983 2113897 0.03575060643272014 0.33578024473912343 chr20 63025520 2456823 0.03898139991546282 0.23726382839700055 chr21 48129895 1517875 0.03153705197154492 0.21930232176529746 chr22 51304566 1269229 0.02473910411794537 0.18439299050236405 chrMT 16571 91695 5.533462072294973 3.6121246211537152 chrX 155270560 7111891 0.045803216012101716 0.25973856534852335 chrY 59373566 287499 0.004842205367957855 0.10308930368513856