BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231765.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 = 4,649,109 number of mapped reads = 4,198,438 (90.31%) number of supplementary alignments = 40,117 (0.86%) number of secondary alignments = 0 number of mapped bases = 288,928,684 bp number of sequenced bases = 288,834,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 905,369 duplication rate = 10.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9794 >>>>>>> ACTG content number of A's = 73,813,332 bp (25.56%) number of C's = 51,020,184 bp (17.66%) number of T's = 79,454,924 bp (27.51%) number of G's = 84,483,252 bp (29.25%) number of N's = 62,441 bp (0.02%) GC percentage = 46.91% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,782,246 number of insertions = 18,386 mapped reads with insertion percentage = 0.43% number of deletions = 58,229 mapped reads with deletion percentage = 1.37% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0933X std coverageData = 54.309X There is a 3.2% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 33041847 0.1325647529680578 0.9590176397253184 chr2 243199373 57439595 0.2361831541399574 193.732611921774 chr3 198022430 11074700 0.055926492771551185 0.5134243694269388 chr4 191154276 16603363 0.08685844411871801 0.6402831612023391 chr5 180915260 14129244 0.07809868553929614 0.6054874270070266 chr6 171115067 6921812 0.040451212867187204 0.533866766031864 chr7 159138663 15969269 0.10034814104225571 2.4058501480122985 chr8 146364022 7724017 0.0527726479120668 0.6844951966828831 chr9 141213431 12432011 0.08803702956555173 0.7438294727410569 chr10 135534747 18192125 0.1342248050973969 1.0363949657876304 chr11 135006516 26308121 0.1948655648591065 2.002365724495346 chr12 133851895 12820069 0.09577801644123156 0.74017030351042 chr13 115169878 7213776 0.06263596111476301 0.5471203452248288 chr14 107349540 6118156 0.056992847850116546 0.6474922081498885 chr15 102531392 8056373 0.07857469642078009 0.693016571608425 chr16 90354753 3930736 0.04350336722186601 0.48457954489255306 chr17 81195210 8422641 0.10373322514961165 1.2658789758932754 chr18 78077248 5014779 0.06422842926021163 1.0627865958625367 chr19 59128983 3920057 0.06629670934810429 0.6796461720031259 chr20 63025520 3058350 0.04852558138354114 0.4887586930178157 chr21 48129895 2140165 0.04446643816696463 0.4812426944500761 chr22 51304566 1558437 0.03037618523076484 0.3684163102417714 chrMT 16571 111085 6.703578540824331 6.66236092537145 chrX 155270560 6231527 0.04013334530383609 0.5843081914238094 chrY 59373566 496429 0.008361111407726461 0.25373048370903