BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926978.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 22,312,588 number of mapped reads = 21,791,789 (97.67%) number of supplementary alignments = 854,532 (3.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,940,986 number of mapped paired reads (second in pair) = 10,850,803 number of mapped paired reads (both in pair) = 21,487,722 number of mapped paired reads (singletons) = 304,067 number of mapped bases = 1,956,137,668 bp number of sequenced bases = 1,954,579,867 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,120,503 duplication rate = 7.72% >>>>>>> Insert size mean insert size = 453,030.7834 std insert size = 6,622,800.3264 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.2859 >>>>>>> ACTG content number of A's = 560,596,864 bp (28.68%) number of C's = 373,016,171 bp (19.08%) number of T's = 575,835,703 bp (29.46%) number of G's = 444,986,335 bp (22.77%) number of N's = 144,794 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 18,753,855 number of insertions = 353,220 mapped reads with insertion percentage = 1.59% number of deletions = 1,054,157 mapped reads with deletion percentage = 4.71% homopolymer indels = 51.72% >>>>>>> Coverage mean coverageData = 0.6319X std coverageData = 2.4X There is a 28.72% of reference with a coverageData >= 1X There is a 14.49% of reference with a coverageData >= 2X There is a 7.49% of reference with a coverageData >= 3X There is a 4.26% of reference with a coverageData >= 4X There is a 2.52% of reference with a coverageData >= 5X There is a 1.56% of reference with a coverageData >= 6X There is a 1% of reference with a coverageData >= 7X There is a 0.66% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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% 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 164797044 0.6611700437849661 2.7907461215294056 chr2 243199373 179689789 0.7388579451641925 3.9886348012181747 chr3 198022430 141289102 0.713500495878169 1.5154248146306042 chr4 191154276 128976576 0.6747250372782663 2.113000646098457 chr5 180915260 117414688 0.6490037822127331 1.4135680899787908 chr6 171115067 120709059 0.7054262439671662 2.141069176539322 chr7 159138663 107006245 0.6724088476224034 2.395233176551254 chr8 146364022 105479066 0.7206625272978628 1.830547035277686 chr9 141213431 83506341 0.5913484320057346 3.0052702388881065 chr10 135534747 69476547 0.5126105927655585 2.8791068644197755 chr11 135006516 96616313 0.7156418509459203 3.260851681095625 chr12 133851895 66154473 0.49423635728130705 1.6361593882413814 chr13 115169878 44423901 0.3857249983368047 1.1810606657507743 chr14 107349540 57999502 0.5402864511575923 1.388512883966018 chr15 102531392 60042442 0.5856005739198391 1.4949854923753192 chr16 90354753 58305309 0.6452932144034526 2.8443647782755077 chr17 81195210 50613102 0.6233508355973215 2.141644195957732 chr18 78077248 55549840 0.7114728224027568 3.2040670013143546 chr19 59128983 30367068 0.5135733181813731 1.833618010702495 chr20 63025520 44655413 0.7085290688597254 1.606742944915329 chr21 48129895 25788724 0.53581508956128 2.0849879248664416 chr22 51304566 23100282 0.4502578191578504 1.2931189160428198 chrMT 16571 338731 20.44119244463219 18.508023642647192 chrX 155270560 120262272 0.7745336398606407 1.8697627002651072 chrY 59373566 3575839 0.06022611139778938 1.8827697878112732