BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618582.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 57,618,328 number of mapped reads = 55,409,245 (96.17%) number of supplementary alignments = 219,818 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,003,694 number of mapped paired reads (second in pair) = 27,405,551 number of mapped paired reads (both in pair) = 54,258,688 number of mapped paired reads (singletons) = 1,150,557 number of mapped bases = 5,232,424,465 bp number of sequenced bases = 5,228,806,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,406,147 duplication rate = 19.42% >>>>>>> Insert size mean insert size = 79,812.4249 std insert size = 2,822,522.1888 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 52.0826 >>>>>>> ACTG content number of A's = 1,425,664,391 bp (27.27%) number of C's = 1,145,456,110 bp (21.91%) number of T's = 1,442,013,295 bp (27.58%) number of G's = 1,215,438,779 bp (23.25%) number of N's = 233,600 bp (0%) GC percentage = 45.15% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 67,788,470 number of insertions = 962,699 mapped reads with insertion percentage = 1.71% number of deletions = 2,638,490 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.43% >>>>>>> Coverage mean coverageData = 1.6902X std coverageData = 6.9783X There is a 27.3% of reference with a coverageData >= 1X There is a 19.19% of reference with a coverageData >= 2X There is a 14.65% of reference with a coverageData >= 3X There is a 11.77% of reference with a coverageData >= 4X There is a 9.72% of reference with a coverageData >= 5X There is a 8.19% of reference with a coverageData >= 6X There is a 7.01% of reference with a coverageData >= 7X There is a 6.08% of reference with a coverageData >= 8X There is a 5.32% of reference with a coverageData >= 9X There is a 4.69% of reference with a coverageData >= 10X There is a 4.17% of reference with a coverageData >= 11X There is a 3.72% of reference with a coverageData >= 12X There is a 3.34% of reference with a coverageData >= 13X There is a 3.01% of reference with a coverageData >= 14X There is a 2.72% of reference with a coverageData >= 15X There is a 2.47% of reference with a coverageData >= 16X There is a 2.25% of reference with a coverageData >= 17X There is a 2.06% of reference with a coverageData >= 18X There is a 1.88% of reference with a coverageData >= 19X There is a 1.73% of reference with a coverageData >= 20X There is a 1.59% of reference with a coverageData >= 21X There is a 1.47% of reference with a coverageData >= 22X There is a 1.36% of reference with a coverageData >= 23X There is a 1.26% of reference with a coverageData >= 24X There is a 1.17% of reference with a coverageData >= 25X There is a 1.08% of reference with a coverageData >= 26X There is a 1.01% of reference with a coverageData >= 27X There is a 0.94% of reference with a coverageData >= 28X There is a 0.88% of reference with a coverageData >= 29X There is a 0.82% of reference with a coverageData >= 30X There is a 0.77% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.63% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.56% of reference with a coverageData >= 36X There is a 0.52% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.47% of reference with a coverageData >= 39X There is a 0.44% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.31% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.28% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 486234138 1.9507840584276819 8.004727070361806 chr2 243199373 465935010 1.9158561317508003 8.306761400851396 chr3 198022430 348189305 1.7583326545381752 5.702146832115168 chr4 191154276 274066000 1.433742449998869 5.492560413693962 chr5 180915260 312937482 1.729746191670067 5.712821407530974 chr6 171115067 292196334 1.707601435237728 5.796192871261049 chr7 159138663 271149553 1.703857176429841 5.7278373910797775 chr8 146364022 268741361 1.8361162622328047 6.493380889893653 chr9 141213431 234569033 1.661095770699035 6.735908986938038 chr10 135534747 274653955 2.0264468048182507 6.57178873892407 chr11 135006516 275563848 2.041115171063299 7.174331003695783 chr12 133851895 247278932 1.847407031480578 6.40333386275415 chr13 115169878 144211040 1.2521593536810034 4.667536193899192 chr14 107349540 166205973 1.5482690750235166 5.822669361702819 chr15 102531392 178011136 1.7361622867657935 6.474854983183895 chr16 90354753 189150137 2.0934165687996513 15.827043316439157 chr17 81195210 171722322 2.1149316813146983 7.445520263956654 chr18 78077248 139984038 1.792891547611924 6.745176610431118 chr19 59128983 111232447 1.8811831585197398 7.462593212337497 chr20 63025520 157214038 2.494450470222221 7.780577723834875 chr21 48129895 68082205 1.4145512887572267 9.104215607812655 chr22 51304566 95338267 1.8582803526688054 7.1885110808699375 chrMT 16571 2174 0.13119304809607146 0.7025067274426534 chrX 155270560 9618445 0.06194635351350571 1.5094433033735508 chrY 59373566 50137292 0.8444379439833545 6.050088797088539