BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960902.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 118,460,170 number of mapped reads = 116,770,635 (98.57%) number of supplementary alignments = 278,972 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 58,469,489 number of mapped paired reads (second in pair) = 58,301,146 number of mapped paired reads (both in pair) = 116,314,252 number of mapped paired reads (singletons) = 456,383 number of mapped bases = 11,528,164,468 bp number of sequenced bases = 11,524,618,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,061,378 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 22,628.7779 std insert size = 1,407,159.4343 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.6397 >>>>>>> ACTG content number of A's = 3,408,920,441 bp (29.58%) number of C's = 2,347,854,382 bp (20.37%) number of T's = 3,393,558,701 bp (29.45%) number of G's = 2,373,984,439 bp (20.6%) number of N's = 300,072 bp (0%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 76,427,526 number of insertions = 1,281,403 mapped reads with insertion percentage = 1.06% number of deletions = 1,400,711 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.42% >>>>>>> Coverage mean coverageData = 3.7239X std coverageData = 41.0894X There is a 85.54% of reference with a coverageData >= 1X There is a 75.47% of reference with a coverageData >= 2X There is a 61.14% of reference with a coverageData >= 3X There is a 46.29% of reference with a coverageData >= 4X There is a 32.55% of reference with a coverageData >= 5X There is a 21.57% of reference with a coverageData >= 6X There is a 13.5% of reference with a coverageData >= 7X There is a 8.08% of reference with a coverageData >= 8X There is a 4.65% of reference with a coverageData >= 9X There is a 2.62% of reference with a coverageData >= 10X There is a 1.47% of reference with a coverageData >= 11X There is a 0.84% of reference with a coverageData >= 12X There is a 0.5% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 936799333 3.7584633861353547 98.80128960421403 chr2 243199373 989660027 4.06933626017202 25.818802909213467 chr3 198022430 761759401 3.846833921793607 8.13879773649529 chr4 191154276 779669464 4.078744563370374 35.34478542242378 chr5 180915260 694469212 3.8386436390164103 4.320880293134807 chr6 171115067 662190164 3.8698530504037962 12.129596804877314 chr7 159138663 615689209 3.868885143266536 25.155592701835428 chr8 146364022 580553956 3.966507260916894 42.040311543366016 chr9 141213431 480691299 3.404005522675814 35.37332373559226 chr10 135534747 600899958 4.433549117850937 94.17580559661292 chr11 135006516 518641055 3.841600171357655 16.273605908632216 chr12 133851895 508460779 3.7986819611332363 4.6475212240625385 chr13 115169878 367832541 3.1938259151407626 2.8698214923521985 chr14 107349540 339705486 3.1644801272553194 3.950519581560709 chr15 102531392 319108297 3.1122984948843766 2.8996223956649874 chr16 90354753 365497206 4.045135356631433 38.30847667134441 chr17 81195210 304261995 3.7472899571292446 15.416491141066661 chr18 78077248 314791988 4.031801786866258 42.58177886155102 chr19 59128983 219886280 3.718756333082881 47.589028609963385 chr20 63025520 235514314 3.7368087403324877 13.65816429190945 chr21 48129895 158176715 3.286454603734332 17.80771923119264 chr22 51304566 132494839 2.5825155406245908 3.493090657374737 chrMT 16571 8932557 539.0475529539557 79.70104590133865 chrX 155270560 594061397 3.825975748396863 12.721633759833459 chrY 59373566 38416996 0.6470387175329843 37.7660826356188