BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716922.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,183,129 number of mapped reads = 1,062,437 (89.8%) number of supplementary alignments = 4,543 (0.38%) number of secondary alignments = 0 number of mapped bases = 60,249,517 bp number of sequenced bases = 60,233,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,723 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5754 >>>>>>> ACTG content number of A's = 15,305,867 bp (25.41%) number of C's = 12,100,537 bp (20.09%) number of T's = 18,451,121 bp (30.63%) number of G's = 14,374,873 bp (23.87%) number of N's = 1,247 bp (0%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 298,946 number of insertions = 3,803 mapped reads with insertion percentage = 0.36% number of deletions = 9,422 mapped reads with deletion percentage = 0.88% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.1816X There is a 1.8% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4999223 0.020057013218033267 0.27434156055012937 chr2 243199373 5216613 0.021449944280900756 0.2031653243627405 chr3 198022430 3901830 0.01970397999862945 0.1490222919019728 chr4 191154276 3834271 0.020058515457953972 0.15780793928994039 chr5 180915260 3708015 0.020495866407289245 0.15246334127539152 chr6 171115067 3509359 0.020508766770374463 0.1599038332332087 chr7 159138663 3188286 0.020034641110438386 0.19646464970176433 chr8 146364022 3031900 0.020714790141528088 0.1712811525830279 chr9 141213431 2586936 0.018319333944941823 0.18181238033820638 chr10 135534747 2792655 0.020604716220852207 0.17716763931488277 chr11 135006516 2800946 0.020746746771837295 0.18281608076743858 chr12 133851895 2778770 0.020760034813104438 0.15373063968001718 chr13 115169878 1966093 0.01707124322906724 0.13778720689147259 chr14 107349540 1794129 0.016712964023879374 0.14341048512367036 chr15 102531392 1800460 0.017560085402917383 0.14115773887810704 chr16 90354753 1800200 0.019923689017223033 0.1584413922773411 chr17 81195210 1655855 0.02039350597159611 0.15869126012190576 chr18 78077248 1624866 0.02081100501902936 0.30105843748611444 chr19 59128983 1054090 0.017826959750009568 0.2100167391598168 chr20 63025520 1235562 0.019604153999840064 0.1515226623552034 chr21 48129895 813901 0.01691050853113226 0.14701049517894613 chr22 51304566 729527 0.01421953359862746 0.12566683782449173 chrMT 16571 424 0.02558686862591274 0.17180950581458332 chrX 155270560 3259069 0.020989613227388373 0.16968622153669252 chrY 59373566 166537 0.00280490142700878 0.07403137058269299