BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174007.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 15,887,078 number of mapped reads = 15,431,059 (97.13%) number of supplementary alignments = 1,677,272 (10.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,732,879 number of mapped paired reads (second in pair) = 7,698,180 number of mapped paired reads (both in pair) = 15,122,722 number of mapped paired reads (singletons) = 308,337 number of mapped bases = 1,819,788,781 bp number of sequenced bases = 1,818,740,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,326,422 duplication rate = 65.6% >>>>>>> Insert size mean insert size = 1,023,216.1851 std insert size = 9,558,023.5323 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.5469 >>>>>>> ACTG content number of A's = 539,773,971 bp (29.68%) number of C's = 363,278,559 bp (19.97%) number of T's = 538,925,899 bp (29.63%) number of G's = 376,740,863 bp (20.71%) number of N's = 21,233 bp (0%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 19,253,274 number of insertions = 194,725 mapped reads with insertion percentage = 1.22% number of deletions = 426,453 mapped reads with deletion percentage = 2.69% homopolymer indels = 43.15% >>>>>>> Coverage mean coverageData = 0.5878X std coverageData = 8.0738X There is a 10.89% of reference with a coverageData >= 1X There is a 8.87% of reference with a coverageData >= 2X There is a 7.11% of reference with a coverageData >= 3X There is a 5.98% of reference with a coverageData >= 4X There is a 4.72% of reference with a coverageData >= 5X There is a 3.9% of reference with a coverageData >= 6X There is a 3.01% of reference with a coverageData >= 7X There is a 2.48% of reference with a coverageData >= 8X There is a 1.9% of reference with a coverageData >= 9X There is a 1.58% of reference with a coverageData >= 10X There is a 1.22% of reference with a coverageData >= 11X There is a 1.04% of reference with a coverageData >= 12X There is a 0.8% of reference with a coverageData >= 13X There is a 0.69% of reference with a coverageData >= 14X There is a 0.54% of reference with a coverageData >= 15X There is a 0.47% of reference with a coverageData >= 16X There is a 0.36% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171764461 0.6891235027253955 5.545642982355798 chr2 243199373 185895840 0.7643763127629445 25.150741308029385 chr3 198022430 126349083 0.6380544012110143 2.405919213658445 chr4 191154276 97083193 0.5078787408344452 3.329153571912658 chr5 180915260 106775533 0.5901963880769372 2.339090753550115 chr6 171115067 105619734 0.6172439157564074 2.6287997954844498 chr7 159138663 124835365 0.7844439726127396 7.315066358020492 chr8 146364022 73922733 0.5050608202062116 3.247108790944941 chr9 141213431 77477998 0.5486588453473664 3.3178522985043104 chr10 135534747 86598874 0.6389422337579602 8.23949593394298 chr11 135006516 76732773 0.5683634781005681 2.498728209832155 chr12 133851895 66144516 0.49416196909277976 2.1408796996778197 chr13 115169878 49152703 0.4267843628348725 1.9777623602701249 chr14 107349540 44319702 0.41285413985006364 1.981873713842633 chr15 102531392 59872767 0.5839457148889581 2.307093059950526 chr16 90354753 70913148 0.7848303010689432 4.626790653576748 chr17 81195210 51651330 0.6361376490066347 3.236691749081477 chr18 78077248 30290251 0.38795233920129973 5.810655048373213 chr19 59128983 38337583 0.6483721020535733 6.2789945270963905 chr20 63025520 70161633 1.113225769497816 3.3140299138893985 chr21 48129895 22013679 0.4573805739655156 2.331332454735584 chr22 51304566 19453817 0.3791829561524797 1.7757977602372068 chrMT 16571 4119755 248.6123348017621 165.65964811297243 chrX 155270560 57747944 0.37191817946686095 1.863255302035452 chrY 59373566 2554366 0.04302194010041438 1.877388924979812