BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617371.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,477,767 (95.24%) number of supplementary alignments = 91,279 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,337,019 number of mapped paired reads (second in pair) = 15,140,748 number of mapped paired reads (both in pair) = 29,922,596 number of mapped paired reads (singletons) = 555,171 number of mapped bases = 2,989,759,214 bp number of sequenced bases = 2,988,867,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,611,748 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 63,907.5278 std insert size = 2,409,916.0209 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.4399 >>>>>>> ACTG content number of A's = 904,080,163 bp (30.25%) number of C's = 594,390,467 bp (19.89%) number of T's = 893,131,135 bp (29.88%) number of G's = 596,527,048 bp (19.96%) number of N's = 738,714 bp (0.02%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 28,821,282 number of insertions = 305,414 mapped reads with insertion percentage = 0.97% number of deletions = 369,574 mapped reads with deletion percentage = 1.18% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.9658X std coverageData = 9.852X There is a 53.33% of reference with a coverageData >= 1X There is a 24.2% of reference with a coverageData >= 2X There is a 9.34% of reference with a coverageData >= 3X There is a 3.29% of reference with a coverageData >= 4X There is a 1.13% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194025903 0.7784369893305101 19.947307799648843 chr2 243199373 295016801 1.2130656315466735 8.911404827880265 chr3 198022430 237510413 1.1994116676580526 1.4842011271311693 chr4 191154276 163245012 0.8539961303298285 9.513796624732532 chr5 180915260 187521812 1.0365173838845878 1.475351678290373 chr6 171115067 139860839 0.817349643441977 3.612767682603357 chr7 159138663 242636896 1.52468854158967 10.952608642438046 chr8 146364022 125734296 0.8590519328581993 7.697677344148463 chr9 141213431 125788852 0.8907711618450798 15.146059321164973 chr10 135534747 125963375 0.9293806775615998 20.18604525400486 chr11 135006516 160854134 1.1914545961618623 5.688352431301061 chr12 133851895 131792998 0.9846180959933365 1.3941790073034543 chr13 115169878 130116878 1.1297821987794412 1.3228643650145335 chr14 107349540 86681993 0.807474284472947 1.385531610556249 chr15 102531392 67329009 0.6566672673282344 1.0746214072871643 chr16 90354753 75133779 0.831542077260728 7.823950583519979 chr17 81195210 93730350 1.1543827523815753 7.173152679012557 chr18 78077248 54105223 0.6929704156580929 15.518898985455005 chr19 59128983 55892269 0.945260110426726 9.529263150511582 chr20 63025520 85826042 1.3617665034735136 2.4755494410720718 chr21 48129895 47557406 0.9881053345327265 3.2830901679002373 chr22 51304566 26754206 0.5214780688330938 0.9305158878356051 chrMT 16571 2043112 123.2944300283628 22.17122669019218 chrX 155270560 124272935 0.8003637972323923 3.059017288177191 chrY 59373566 10364681 0.17456726449612273 8.561525661878024