BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238611.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 = 3,730,340 number of mapped reads = 2,997,125 (80.34%) number of supplementary alignments = 25,622 (0.69%) number of secondary alignments = 0 number of mapped bases = 186,233,442 bp number of sequenced bases = 186,164,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,333,257 duplication rate = 20.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8847 >>>>>>> ACTG content number of A's = 47,187,429 bp (25.35%) number of C's = 32,676,338 bp (17.55%) number of T's = 62,672,765 bp (33.67%) number of G's = 43,623,195 bp (23.43%) number of N's = 4,404 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 946,757 number of insertions = 11,351 mapped reads with insertion percentage = 0.38% number of deletions = 40,460 mapped reads with deletion percentage = 1.34% homopolymer indels = 43.2% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 1.4008X There is a 1.2% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 14499569 0.05817264944748122 0.9279315680158245 chr2 243199373 15496739 0.06372030819339325 2.0099447549656215 chr3 198022430 8390087 0.04236937704481255 0.7700683818532424 chr4 191154276 5310032 0.027778776970701927 0.5861277161007333 chr5 180915260 6980312 0.038583323485260446 0.7109321710057609 chr6 171115067 32264218 0.188552759062415 1.9620567241859088 chr7 159138663 9010350 0.05661949038744909 1.6305754523986415 chr8 146364022 6302151 0.04305806108553098 1.1987708062580629 chr9 141213431 7149385 0.050628222467025814 0.9031920573504174 chr10 135534747 6704071 0.04946385446087858 0.8514258308445058 chr11 135006516 3428208 0.025392907702321568 0.5589494013649187 chr12 133851895 3713751 0.027745225422471605 0.6198985620308312 chr13 115169878 9898385 0.08594595368070113 1.3669230481621009 chr14 107349540 3852629 0.03588864004447527 0.7893668831924071 chr15 102531392 2246256 0.021907983069224302 0.6512516668198234 chr16 90354753 2084454 0.02306966629635964 0.5720326320254056 chr17 81195210 3685324 0.045388441017641314 0.7709959230266901 chr18 78077248 9182305 0.11760538742349115 5.092681949863558 chr19 59128983 4640892 0.07848760057314025 1.127153216667753 chr20 63025520 2494072 0.039572414475913885 0.7492486961316912 chr21 48129895 896858 0.0186341150339098 0.4678563234439072 chr22 51304566 2183542 0.04256038341694578 0.7539300530182479 chrMT 16571 35953 2.169633697423209 4.734184290474289 chrX 155270560 25236142 0.1625301151744413 1.6076017200536392 chrY 59373566 547757 0.009225603865531675 0.531040622269328