BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328252.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 479,260,756 number of mapped reads = 449,799,049 (93.85%) number of supplementary alignments = 20,603,882 (4.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 226,293,414 number of mapped paired reads (second in pair) = 223,505,635 number of mapped paired reads (both in pair) = 445,793,370 number of mapped paired reads (singletons) = 4,005,679 number of mapped bases = 62,301,544,161 bp number of sequenced bases = 62,246,514,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,900,720 duplication rate = 33.21% >>>>>>> Insert size mean insert size = 157,170.1105 std insert size = 3,832,998.1974 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 53.828 >>>>>>> ACTG content number of A's = 17,983,578,407 bp (28.89%) number of C's = 13,118,042,200 bp (21.07%) number of T's = 17,857,552,248 bp (28.69%) number of G's = 13,282,604,106 bp (21.34%) number of N's = 4,737,588 bp (0.01%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 565,258,311 number of insertions = 10,909,302 mapped reads with insertion percentage = 2.3% number of deletions = 30,546,552 mapped reads with deletion percentage = 6.51% homopolymer indels = 44.46% >>>>>>> Coverage mean coverageData = 20.1252X std coverageData = 232.9509X There is a 92.28% of reference with a coverageData >= 1X There is a 92.16% of reference with a coverageData >= 2X There is a 91.98% of reference with a coverageData >= 3X There is a 91.68% of reference with a coverageData >= 4X There is a 91.24% of reference with a coverageData >= 5X There is a 90.6% of reference with a coverageData >= 6X There is a 89.72% of reference with a coverageData >= 7X There is a 88.56% of reference with a coverageData >= 8X There is a 87.07% of reference with a coverageData >= 9X There is a 85.22% of reference with a coverageData >= 10X There is a 82.98% of reference with a coverageData >= 11X There is a 80.33% of reference with a coverageData >= 12X There is a 77.27% of reference with a coverageData >= 13X There is a 73.82% of reference with a coverageData >= 14X There is a 70.01% of reference with a coverageData >= 15X There is a 65.89% of reference with a coverageData >= 16X There is a 61.53% of reference with a coverageData >= 17X There is a 57% of reference with a coverageData >= 18X There is a 52.38% of reference with a coverageData >= 19X There is a 47.76% of reference with a coverageData >= 20X There is a 43.19% of reference with a coverageData >= 21X There is a 38.76% of reference with a coverageData >= 22X There is a 34.51% of reference with a coverageData >= 23X There is a 30.51% of reference with a coverageData >= 24X There is a 26.77% of reference with a coverageData >= 25X There is a 23.34% of reference with a coverageData >= 26X There is a 20.21% of reference with a coverageData >= 27X There is a 17.39% of reference with a coverageData >= 28X There is a 14.87% of reference with a coverageData >= 29X There is a 12.66% of reference with a coverageData >= 30X There is a 10.72% of reference with a coverageData >= 31X There is a 9.04% of reference with a coverageData >= 32X There is a 7.59% of reference with a coverageData >= 33X There is a 6.35% of reference with a coverageData >= 34X There is a 5.3% of reference with a coverageData >= 35X There is a 4.42% of reference with a coverageData >= 36X There is a 3.68% of reference with a coverageData >= 37X There is a 3.07% of reference with a coverageData >= 38X There is a 2.56% of reference with a coverageData >= 39X There is a 2.13% of reference with a coverageData >= 40X There is a 1.79% of reference with a coverageData >= 41X There is a 1.51% of reference with a coverageData >= 42X There is a 1.28% of reference with a coverageData >= 43X There is a 1.09% of reference with a coverageData >= 44X There is a 0.93% of reference with a coverageData >= 45X There is a 0.81% of reference with a coverageData >= 46X There is a 0.71% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.56% of reference with a coverageData >= 49X There is a 0.5% of reference with a coverageData >= 50X There is a 0.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5124246475 20.558610664404323 541.2284859419902 chr2 243199373 5437300032 22.35737685063851 180.96394261888216 chr3 198022430 4149771046 20.956065663874544 24.282241518754667 chr4 191154276 4154908998 21.735893566932294 168.2759273437178 chr5 180915260 3772246648 20.850903610894957 15.896480385059292 chr6 171115067 3582801387 20.93796560299392 65.36304810967975 chr7 159138663 3419772948 21.489265295637175 163.22617272584105 chr8 146364022 3157891712 21.575600812609537 306.4506187918903 chr9 141213431 2684691521 19.011587651319086 276.8293923401048 chr10 135534747 3295877343 24.31758214002495 468.4298954171121 chr11 135006516 2840725459 21.041395209398633 75.74135849689799 chr12 133851895 2782492951 20.787848771210896 14.156625946908761 chr13 115169878 1977311969 17.168655583710873 12.228842722483412 chr14 107349540 1891703272 17.621903847934515 19.417000254962513 chr15 102531392 1747129140 17.039943630142073 12.301150464329341 chr16 90354753 2077683918 22.994738505897967 213.1300643600128 chr17 81195210 1733602504 21.351044033262554 83.78010109876448 chr18 78077248 1741150043 22.30035109587879 265.15522632605627 chr19 59128983 1271873892 21.510160118938625 297.88942295083257 chr20 63025520 1308712027 20.764795387646146 49.08017336829118 chr21 48129895 867900220 18.03245612731962 104.33819152387538 chr22 51304566 784883851 15.298518478842604 86.46087457741994 chrMT 16571 186395621 11248.302516444392 1712.5089746116037 chrX 155270560 1677631014 10.804566004012608 31.83052459877829 chrY 59373566 632840170 10.658618180353189 204.95599314005827