BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617388.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 = 30,661,226 (95.82%) number of supplementary alignments = 98,531 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,408,403 number of mapped paired reads (second in pair) = 15,252,823 number of mapped paired reads (both in pair) = 30,155,416 number of mapped paired reads (singletons) = 505,810 number of mapped bases = 3,009,096,532 bp number of sequenced bases = 3,008,196,616 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,634,887 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 70,455.365 std insert size = 2,542,984.447 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 53.4455 >>>>>>> ACTG content number of A's = 910,004,433 bp (30.25%) number of C's = 597,822,345 bp (19.87%) number of T's = 899,389,300 bp (29.9%) number of G's = 599,994,626 bp (19.95%) number of N's = 985,912 bp (0.03%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 26,379,205 number of insertions = 308,203 mapped reads with insertion percentage = 0.97% number of deletions = 370,541 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.972X std coverageData = 9.9346X There is a 53.65% of reference with a coverageData >= 1X There is a 24.38% of reference with a coverageData >= 2X There is a 9.4% of reference with a coverageData >= 3X There is a 3.3% 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 0.08% 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 195207210 0.7831764238613471 20.06987009727362 chr2 243199373 297010814 1.2212647192967887 9.084731004442462 chr3 198022430 239318119 1.208540461805261 1.4851292962568936 chr4 191154276 164468209 0.8603951344515045 9.823439942889285 chr5 180915260 188813908 1.043659379534927 1.4676705063917328 chr6 171115067 140667718 0.82206506105041 3.700000009233209 chr7 159138663 244260520 1.534891115680669 10.901589666330231 chr8 146364022 126560967 0.8646999807097403 7.836044770206156 chr9 141213431 126964149 0.8990940033175739 15.309090756551383 chr10 135534747 126897945 0.9362761049017194 20.239262275892003 chr11 135006516 161381031 1.1953573485297555 5.603411652060908 chr12 133851895 132703960 0.9914238420008921 1.4387302476110981 chr13 115169878 130774873 1.135495454809807 1.3419593473641964 chr14 107349540 87017312 0.8105979028880794 1.3828440591016045 chr15 102531392 67884499 0.6620850227021203 1.1346627379791918 chr16 90354753 75605312 0.8367607623253643 7.8488866939284065 chr17 81195210 94218610 1.1603961613006482 7.448217130106116 chr18 78077248 54380620 0.6964976531959733 15.652511682755618 chr19 59128983 56394212 0.953749060760947 9.577448716476926 chr20 63025520 86454894 1.3717442394763264 2.432698500932864 chr21 48129895 47913270 0.9954991590985187 3.300001664373841 chr22 51304566 26828442 0.5229250355611623 0.9364164608926274 chrMT 16571 2062829 124.48427976585602 20.954101942710846 chrX 155270560 124879636 0.8042711767124431 3.02550704838624 chrY 59373566 10427473 0.17562483951191343 8.645121552956965