BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080771.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 10,142,107 number of mapped reads = 6,756,020 (66.61%) number of supplementary alignments = 45,369 (0.45%) number of secondary alignments = 0 number of mapped bases = 429,205,266 bp number of sequenced bases = 429,058,582 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 748,592 duplication rate = 8.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.468 >>>>>>> ACTG content number of A's = 131,337,441 bp (30.61%) number of C's = 87,178,813 bp (20.32%) number of T's = 113,136,130 bp (26.37%) number of G's = 97,268,057 bp (22.67%) number of N's = 138,141 bp (0.03%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 3,542,090 number of insertions = 31,014 mapped reads with insertion percentage = 0.46% number of deletions = 78,956 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.89% >>>>>>> Coverage mean coverageData = 0.1386X std coverageData = 0.7947X There is a 9.01% of reference with a coverageData >= 1X There is a 2.71% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% 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% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% 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 54067853 0.21692163808089368 1.2452032029358375 chr2 243199373 30314557 0.12464899323568568 0.7286047156503707 chr3 198022430 25890219 0.1307438707827189 0.5299697916166082 chr4 191154276 24612989 0.12875981387934005 0.6560930775461206 chr5 180915260 30430838 0.16820492643904114 0.6057045650035748 chr6 171115067 28684676 0.16763384138463974 0.93535602168773 chr7 159138663 27713823 0.17414889931556105 1.169020609520043 chr8 146364022 18999625 0.12981076046133797 1.0459073916124533 chr9 141213431 15520974 0.1099114573598881 0.6067821548870382 chr10 135534747 18246366 0.1346250050549768 0.8816173490263383 chr11 135006516 17643842 0.13068881801230986 0.6883912924701077 chr12 133851895 16268321 0.12153971372612991 0.5829525840630866 chr13 115169878 16593559 0.14407898391626325 0.5578570832505619 chr14 107349540 12027013 0.11203599940903333 0.5726753853747675 chr15 102531392 13324653 0.12995681361665312 0.5451684847288355 chr16 90354753 12206049 0.13509028130484735 0.6343829532125907 chr17 81195210 11255665 0.13862474153339835 0.5874179013453923 chr18 78077248 6063321 0.07765797534257354 0.8837562153316153 chr19 59128983 7949938 0.13445078194563231 1.180205576475238 chr20 63025520 8721498 0.13838042113734247 0.5821748511846666 chr21 48129895 6980218 0.14502873941445332 0.7027446048702163 chr22 51304566 2967604 0.0578428828342491 0.35235044152836975 chrMT 16571 53798 3.246514996077485 3.4921561164957553 chrX 155270560 21403588 0.1378470458276186 0.5789599764816902 chrY 59373566 1264279 0.021293634274889266 0.6356650461416742