BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362019.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 = 2,180,347,088 number of mapped reads = 2,149,537,308 (98.59%) number of supplementary alignments = 86,319,000 (3.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,076,641,466 number of mapped paired reads (second in pair) = 1,072,895,842 number of mapped paired reads (both in pair) = 2,134,694,382 number of mapped paired reads (singletons) = 14,842,926 number of mapped bases = 299,442,819,424 bp number of sequenced bases = 299,152,668,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,061,375,812 duplication rate = 45.11% >>>>>>> Insert size mean insert size = 87,951.2161 std insert size = 2,951,531.5359 median insert size = 269 >>>>>>> Mapping quality mean mapping quality = 53.9714 >>>>>>> ACTG content number of A's = 86,395,910,276 bp (28.88%) number of C's = 62,450,146,518 bp (20.88%) number of T's = 85,657,886,188 bp (28.63%) number of G's = 64,643,135,442 bp (21.61%) number of N's = 5,590,465 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 2,317,663,662 number of insertions = 52,047,432 mapped reads with insertion percentage = 2.3% number of deletions = 176,361,313 mapped reads with deletion percentage = 7.84% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 96.7288X std coverageData = 1,594.4582X There is a 92.39% of reference with a coverageData >= 1X There is a 92.38% of reference with a coverageData >= 2X There is a 92.37% of reference with a coverageData >= 3X There is a 92.36% of reference with a coverageData >= 4X There is a 92.36% of reference with a coverageData >= 5X There is a 92.35% of reference with a coverageData >= 6X There is a 92.34% of reference with a coverageData >= 7X There is a 92.33% of reference with a coverageData >= 8X There is a 92.33% of reference with a coverageData >= 9X There is a 92.32% of reference with a coverageData >= 10X There is a 92.31% of reference with a coverageData >= 11X There is a 92.3% of reference with a coverageData >= 12X There is a 92.29% of reference with a coverageData >= 13X There is a 92.29% of reference with a coverageData >= 14X There is a 92.28% of reference with a coverageData >= 15X There is a 92.27% of reference with a coverageData >= 16X There is a 92.26% of reference with a coverageData >= 17X There is a 92.25% of reference with a coverageData >= 18X There is a 92.23% of reference with a coverageData >= 19X There is a 92.22% of reference with a coverageData >= 20X There is a 92.21% of reference with a coverageData >= 21X There is a 92.19% of reference with a coverageData >= 22X There is a 92.18% of reference with a coverageData >= 23X There is a 92.16% of reference with a coverageData >= 24X There is a 92.13% of reference with a coverageData >= 25X There is a 92.11% of reference with a coverageData >= 26X There is a 92.08% of reference with a coverageData >= 27X There is a 92.04% of reference with a coverageData >= 28X There is a 92% of reference with a coverageData >= 29X There is a 91.95% of reference with a coverageData >= 30X There is a 91.89% of reference with a coverageData >= 31X There is a 91.83% of reference with a coverageData >= 32X There is a 91.76% of reference with a coverageData >= 33X There is a 91.67% of reference with a coverageData >= 34X There is a 91.58% of reference with a coverageData >= 35X There is a 91.47% of reference with a coverageData >= 36X There is a 91.36% of reference with a coverageData >= 37X There is a 91.23% of reference with a coverageData >= 38X There is a 91.09% of reference with a coverageData >= 39X There is a 90.94% of reference with a coverageData >= 40X There is a 90.78% of reference with a coverageData >= 41X There is a 90.61% of reference with a coverageData >= 42X There is a 90.43% of reference with a coverageData >= 43X There is a 90.24% of reference with a coverageData >= 44X There is a 90.04% of reference with a coverageData >= 45X There is a 89.84% of reference with a coverageData >= 46X There is a 89.62% of reference with a coverageData >= 47X There is a 89.4% of reference with a coverageData >= 48X There is a 89.18% of reference with a coverageData >= 49X There is a 88.95% of reference with a coverageData >= 50X There is a 88.72% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 24987963288 100.25236120876104 2109.7963439116133 chr2 243199373 26625153834 109.4787108435514 4697.0316064671815 chr3 198022430 19925104275 100.62044120456456 86.78448577047538 chr4 191154276 19699129564 103.05356477612878 821.7674653729191 chr5 180915260 18079494426 99.9334960798774 69.00603743703591 chr6 171115067 17366469223 101.49000627162773 322.3961963301092 chr7 159138663 16514150275 103.77208130119831 642.2346029007258 chr8 146364022 14976260479 102.32200696835183 1249.6485265776796 chr9 141213431 12838286859 90.91406368421146 1021.6243479904851 chr10 135534747 15474176459 114.171286710706 1906.491424378243 chr11 135006516 13681649053 101.34065716502158 281.16213169376294 chr12 133851895 13619022453 101.74695287653567 262.5699282114433 chr13 115169878 9450585176 82.05778576929637 51.873409805784505 chr14 107349540 9120316608 84.9590655721487 102.96762702809104 chr15 102531392 8605772138 83.93304694429585 85.93241329457491 chr16 90354753 9355103137 103.5374767390488 513.2426630291782 chr17 81195210 8813887658 108.55181799517484 412.4500829128733 chr18 78077248 8111747864 103.89387525543933 966.1005386305532 chr19 59128983 6587919850 111.41608591509176 1204.4217249143198 chr20 63025520 6390340567 101.39290508035475 237.6262706249231 chr21 48129895 4137720743 85.96986847779327 422.47255339909196 chr22 51304566 3925352669 76.51078597955589 295.944849807565 chrMT 16571 506606095 30571.848108140726 4134.754749328726 chrX 155270560 8121012296 52.30233146579751 128.9874175767247 chrY 59373566 2529594435 42.604724718741 986.5968765480272