BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013340.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 = 2,637,433 number of mapped reads = 2,372,321 (89.95%) number of supplementary alignments = 18,062 (0.68%) number of secondary alignments = 0 number of mapped bases = 157,238,915 bp number of sequenced bases = 157,179,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,302 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0848 >>>>>>> ACTG content number of A's = 43,040,712 bp (27.38%) number of C's = 29,829,878 bp (18.98%) number of T's = 48,763,398 bp (31.02%) number of G's = 35,507,837 bp (22.59%) number of N's = 37,887 bp (0.02%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,245,213 number of insertions = 10,385 mapped reads with insertion percentage = 0.43% number of deletions = 34,684 mapped reads with deletion percentage = 1.45% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.4599X There is a 4.29% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 12605557 0.05057382384616005 0.9654280305495578 chr2 243199373 16179325 0.06652700128466203 0.509531843232289 chr3 198022430 9293459 0.0469313451006535 0.24607373137432734 chr4 191154276 10284862 0.05380398605365229 0.27199534824277777 chr5 180915260 7249783 0.04007281088394644 0.2294274853831447 chr6 171115067 6318706 0.03692664889644113 0.28045909163845556 chr7 159138663 7937467 0.049877678059919356 0.7263047998594663 chr8 146364022 7443135 0.05085358340316721 0.4279510308777825 chr9 141213431 5367608 0.0380106053793141 0.34926271553094773 chr10 135534747 7952169 0.05867254837610019 0.4424290076174991 chr11 135006516 5406100 0.04004325243086786 0.2983238946801244 chr12 133851895 8431857 0.06299393071723042 0.29237387544486754 chr13 115169878 5881062 0.051064237473621356 0.2610447388036453 chr14 107349540 4561912 0.04249586910200081 0.261798937625726 chr15 102531392 4729922 0.0461314521117591 0.24422477891231428 chr16 90354753 6311229 0.06984944112458588 0.3310970100248585 chr17 81195210 5307221 0.06536372034754268 0.33690920732420465 chr18 78077248 4359063 0.055830131205444125 0.6289127269034298 chr19 59128983 3336578 0.056428807510523225 0.6941832993639849 chr20 63025520 3242540 0.051448048346130267 0.26680938181240693 chr21 48129895 2079611 0.04320830120240238 0.25322510190416925 chr22 51304566 2055068 0.040056239828634356 0.22852941048412706 chrMT 16571 238000 14.362440407941584 8.673281130540218 chrX 155270560 10319579 0.0664619165410365 0.3246602817970152 chrY 59373566 347102 0.005846069612864419 0.1168286112074984