BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004023.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,265,577 number of mapped reads = 1,785,878 (78.83%) number of supplementary alignments = 16,028 (0.71%) number of secondary alignments = 0 number of mapped bases = 114,592,091 bp number of sequenced bases = 114,537,819 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,324 duplication rate = 6.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5104 >>>>>>> ACTG content number of A's = 30,696,328 bp (26.8%) number of C's = 21,710,369 bp (18.95%) number of T's = 35,553,582 bp (31.04%) number of G's = 26,554,700 bp (23.18%) number of N's = 22,840 bp (0.02%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,036,430 number of insertions = 8,723 mapped reads with insertion percentage = 0.48% number of deletions = 33,420 mapped reads with deletion percentage = 1.85% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.324X There is a 2.54% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 10261257 0.04116843103070945 0.43059472489349054 chr2 243199373 9625929 0.03958040220769812 0.44530506877909576 chr3 198022430 7673091 0.0387485952980175 0.26863664761747114 chr4 191154276 7848167 0.041056716931616014 0.28142008484199005 chr5 180915260 6783959 0.037497992153895696 0.2649476288878569 chr6 171115067 6860187 0.040091075089255586 0.30892300925135796 chr7 159138663 6302732 0.03960528435506587 0.4096499995589419 chr8 146364022 6483134 0.04429458764121691 0.33948614770377444 chr9 141213431 4224568 0.02991619118722496 0.28166615017570157 chr10 135534747 5479272 0.04042706480279924 0.3091732015695676 chr11 135006516 5002281 0.03705214494980376 0.322270033269206 chr12 133851895 4793069 0.03580874966320051 0.26155272920831796 chr13 115169878 3231799 0.028061148072067943 0.2320502967008733 chr14 107349540 3201154 0.029819913527342548 0.25321922401512215 chr15 102531392 3270439 0.031896953081452364 0.2519733850600536 chr16 90354753 3387852 0.037495005935105595 0.27500456794931105 chr17 81195210 2995264 0.036889663811448974 0.2790345265883789 chr18 78077248 3026545 0.03876346922473497 0.44386234965260507 chr19 59128983 2198290 0.03717787603416078 0.3577316345022582 chr20 63025520 2884374 0.045765175757375744 0.3044158921417615 chr21 48129895 1543078 0.03206069741062182 0.25715668335361425 chr22 51304566 1229445 0.023963656568111308 0.21173095463100775 chrMT 16571 95569 5.76724398044777 5.227175341959993 chrX 155270560 5903214 0.038018887804616666 0.2822226124846758 chrY 59373566 287422 0.004840908494531051 0.11153904145409253