BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006022.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 23,799,268 number of mapped reads = 16,905,843 (71.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,528,584 number of mapped paired reads (second in pair) = 8,377,259 number of mapped paired reads (both in pair) = 15,035,856 number of mapped paired reads (singletons) = 1,869,987 number of mapped bases = 653,298,188 bp number of sequenced bases = 653,224,444 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 899,767 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 64,719.4627 std insert size = 2,445,876.1218 median insert size = 92 >>>>>>> Mapping quality mean mapping quality = 47.268 >>>>>>> ACTG content number of A's = 190,592,237 bp (29.18%) number of C's = 134,792,849 bp (20.63%) number of T's = 191,032,002 bp (29.24%) number of G's = 136,727,722 bp (20.93%) number of N's = 79,634 bp (0.01%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 3,874,363 number of insertions = 19,375 mapped reads with insertion percentage = 0.11% number of deletions = 58,089 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 0.211X std coverageData = 1.0658X There is a 13.4% of reference with a coverageData >= 1X There is a 4.67% of reference with a coverageData >= 2X There is a 1.63% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% 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% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 53869269 0.21612491388737604 1.6695647163128655 chr2 243199373 56581929 0.2326565578768988 0.962097767934722 chr3 198022430 47254761 0.23863337602715007 0.6891814902008485 chr4 191154276 42242153 0.22098460931106767 0.7909249780117774 chr5 180915260 38099101 0.21059086447434008 0.6528789122467801 chr6 171115067 36887202 0.21556957342628397 0.9677810549217517 chr7 159138663 36666341 0.23040498335718707 1.4843387105376995 chr8 146364022 33776581 0.230771063396987 2.2072318734871206 chr9 141213431 25850452 0.18305944283727515 0.8138561538406333 chr10 135534747 31164560 0.22993778857313985 1.1945003498164262 chr11 135006516 29565602 0.21899388915420942 0.8394983518798153 chr12 133851895 29878851 0.2232232199626311 0.677468369913718 chr13 115169878 22538037 0.19569385147738022 0.6244682550186286 chr14 107349540 19690600 0.1834250989803962 0.672018751221606 chr15 102531392 17887143 0.17445528292447254 0.5887450895647061 chr16 90354753 18848340 0.20860374661197956 0.8200243417361027 chr17 81195210 17107965 0.21070165345960679 0.7292835751154018 chr18 78077248 16898568 0.21643396037729198 1.1891118787234678 chr19 59128983 11922406 0.2016338755564255 1.3203335568180161 chr20 63025520 12553607 0.19918291828452983 0.6667749528222303 chr21 48129895 8413861 0.17481569407122122 0.7101754408500364 chr22 51304566 7117411 0.13872860750834537 0.5371399825867037 chrMT 16571 41073 2.478607205358759 2.538640349110315 chrX 155270560 36843061 0.23728297882096902 0.8198979736135857 chrY 59373566 1599314 0.02693646529501024 0.5336394562853392