BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927027.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 = 9,385,318 number of mapped reads = 9,181,284 (97.83%) number of supplementary alignments = 303,931 (3.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,601,425 number of mapped paired reads (second in pair) = 4,579,859 number of mapped paired reads (both in pair) = 9,053,364 number of mapped paired reads (singletons) = 127,920 number of mapped bases = 845,069,951 bp number of sequenced bases = 844,422,660 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 502,718 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 350,574.9436 std insert size = 5,780,473.8518 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.3585 >>>>>>> ACTG content number of A's = 241,643,532 bp (28.62%) number of C's = 165,987,206 bp (19.66%) number of T's = 245,880,266 bp (29.12%) number of G's = 190,748,792 bp (22.59%) number of N's = 162,864 bp (0.02%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 7,907,506 number of insertions = 146,934 mapped reads with insertion percentage = 1.57% number of deletions = 439,084 mapped reads with deletion percentage = 4.66% homopolymer indels = 51.75% >>>>>>> Coverage mean coverageData = 0.273X std coverageData = 1.3673X There is a 17.14% of reference with a coverageData >= 1X There is a 6.11% of reference with a coverageData >= 2X There is a 2.09% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% 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 67303447 0.2700231868228726 1.791815135242543 chr2 243199373 73841267 0.3036244135382701 2.071195492519193 chr3 198022430 58110662 0.2934549485126508 0.7658892920031554 chr4 191154276 51957410 0.27180877711571566 0.9666744670935473 chr5 180915260 51915899 0.28696252046400067 0.7358158055978081 chr6 171115067 49022238 0.286486975457281 0.821648022050459 chr7 159138663 44138034 0.27735581767455214 1.0009303860107834 chr8 146364022 43494332 0.2971654605118736 0.8655354276668419 chr9 141213431 36046212 0.25526050705474324 1.586707659656533 chr10 135534747 42292493 0.31204170101118056 3.123093442069434 chr11 135006516 39920993 0.2956967869610086 1.4741264814858683 chr12 133851895 37905395 0.28318907999023846 0.7434732159712572 chr13 115169878 25407987 0.2206131276790968 0.6418323419005355 chr14 107349540 24829413 0.2312950106726121 0.6746287018722437 chr15 102531392 24161249 0.23564733228239015 0.6787269450216341 chr16 90354753 26749594 0.29605076779967515 2.0342962955355803 chr17 81195210 21264368 0.26189190224398706 0.8121968906385293 chr18 78077248 22741922 0.2912746361142237 1.5931795107199533 chr19 59128983 13401876 0.2266549384081238 1.1650614674902697 chr20 63025520 18791430 0.2981558898681042 0.7921380401204516 chr21 48129895 10946424 0.22743502764757745 0.8734002037063288 chr22 51304566 10117518 0.19720502069932722 0.6485989618525758 chrMT 16571 19962 1.2046346026190333 1.6310456450952402 chrX 155270560 49100258 0.3162238739913091 0.9005453007784259 chrY 59373566 1589568 0.02677231817270332 0.8487824895381247