BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716979.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 = 4,093,315 number of mapped reads = 3,470,381 (84.78%) number of supplementary alignments = 12,831 (0.31%) number of secondary alignments = 0 number of mapped bases = 196,246,406 bp number of sequenced bases = 196,189,914 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,631 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2028 >>>>>>> ACTG content number of A's = 49,805,870 bp (25.39%) number of C's = 35,861,910 bp (18.28%) number of T's = 60,634,555 bp (30.91%) number of G's = 49,884,501 bp (25.43%) number of N's = 3,078 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,016,560 number of insertions = 13,484 mapped reads with insertion percentage = 0.39% number of deletions = 35,905 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0634X std coverageData = 0.5466X There is a 5.24% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 14493621 0.05814878591616428 0.6303014838966094 chr2 243199373 17785486 0.07313129873899799 0.7123086597657328 chr3 198022430 15227237 0.07689652631775097 0.3760438011612606 chr4 191154276 11028072 0.05769199743143596 0.30915071167545477 chr5 180915260 9912463 0.054790640656846745 0.27585471877965906 chr6 171115067 12415018 0.07255362264504739 0.3879949508589956 chr7 159138663 12263592 0.07706230383498949 1.4234803098136728 chr8 146364022 15477284 0.1057451400180845 0.4996147415944972 chr9 141213431 8096569 0.05733568643339598 0.3601087507071698 chr10 135534747 9369163 0.06912738768014966 0.7212697018113983 chr11 135006516 6615650 0.04900244962991268 0.36348482674447385 chr12 133851895 9258709 0.06917129563238533 0.3468066638590757 chr13 115169878 5142863 0.04465458407449212 0.2470940365963047 chr14 107349540 4972625 0.04632181004222282 0.27278159159765414 chr15 102531392 4649214 0.045344298066293684 0.2642296001426434 chr16 90354753 5952718 0.06588162550784683 0.3350931288483498 chr17 81195210 8158463 0.10047960957302776 0.4090136793319444 chr18 78077248 4751676 0.06085865116557387 0.610531188153012 chr19 59128983 3933246 0.06651976408929611 0.6589826245552669 chr20 63025520 4346792 0.06896876059094792 0.32506303890337324 chr21 48129895 1996677 0.0414851725730962 0.2564649514599869 chr22 51304566 2759649 0.05378953990177015 0.27803628222600774 chrMT 16571 129051 7.787761752459115 5.840722903896654 chrX 155270560 7070621 0.045537421904062174 0.3258361797798341 chrY 59373566 439947 0.007409812642885556 0.16679325660727412