BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617723.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 42,586,162 number of mapped reads = 41,723,338 (97.97%) number of supplementary alignments = 997,218 (2.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,082,071 number of mapped paired reads (second in pair) = 20,641,267 number of mapped paired reads (both in pair) = 41,207,092 number of mapped paired reads (singletons) = 516,246 number of mapped bases = 5,553,885,933 bp number of sequenced bases = 5,549,451,081 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,247,308 duplication rate = 25.6% >>>>>>> Insert size mean insert size = 148,446.0254 std insert size = 3,686,015.7362 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 53.3302 >>>>>>> ACTG content number of A's = 1,604,100,845 bp (28.91%) number of C's = 1,054,652,441 bp (19%) number of T's = 1,657,727,074 bp (29.87%) number of G's = 1,232,739,731 bp (22.21%) number of N's = 230,990 bp (0%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 66,192,027 number of insertions = 1,019,682 mapped reads with insertion percentage = 2.29% number of deletions = 2,229,935 mapped reads with deletion percentage = 5.12% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 1.7941X std coverageData = 20.3181X There is a 37.31% of reference with a coverageData >= 1X There is a 26.94% of reference with a coverageData >= 2X There is a 19.85% of reference with a coverageData >= 3X There is a 15.31% of reference with a coverageData >= 4X There is a 11.92% of reference with a coverageData >= 5X There is a 9.48% of reference with a coverageData >= 6X There is a 7.6% of reference with a coverageData >= 7X There is a 6.17% of reference with a coverageData >= 8X There is a 5.05% of reference with a coverageData >= 9X There is a 4.17% of reference with a coverageData >= 10X There is a 3.46% of reference with a coverageData >= 11X There is a 2.89% of reference with a coverageData >= 12X There is a 2.43% of reference with a coverageData >= 13X There is a 2.05% of reference with a coverageData >= 14X There is a 1.75% of reference with a coverageData >= 15X There is a 1.49% of reference with a coverageData >= 16X There is a 1.28% of reference with a coverageData >= 17X There is a 1.1% of reference with a coverageData >= 18X There is a 0.95% of reference with a coverageData >= 19X There is a 0.82% of reference with a coverageData >= 20X There is a 0.72% of reference with a coverageData >= 21X There is a 0.63% of reference with a coverageData >= 22X There is a 0.55% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 543196615 2.179319003582342 20.11103156675385 chr2 243199373 484733146 1.9931512981326642 27.28958868853037 chr3 198022430 291029401 1.4696789702055468 3.457636994605484 chr4 191154276 280122027 1.4654238077310915 13.304246930140012 chr5 180915260 299562744 1.6558180000957354 4.256547337946892 chr6 171115067 394839704 2.3074514180565995 12.500670153891594 chr7 159138663 357621933 2.2472347464676137 26.256919019761554 chr8 146364022 343890108 2.3495535535365377 7.716789418969445 chr9 141213431 192443903 1.3627875311662103 36.3896730552969 chr10 135534747 194680028 1.4363846342665176 36.6396846455537 chr11 135006516 276646052 2.049131110086568 22.377724757067618 chr12 133851895 260620525 1.947081324474338 8.263561208819802 chr13 115169878 104833141 0.9102479122188529 2.5579860215357177 chr14 107349540 199904614 1.8621841695828412 4.8958051497568835 chr15 102531392 145660928 1.4206471321485619 4.480870932272761 chr16 90354753 106966857 1.18385423509486 14.932196769937498 chr17 81195210 170623923 2.1014038020223116 36.52915955033859 chr18 78077248 193605935 2.479671606765648 33.80909425178502 chr19 59128983 86467666 1.4623567261422372 9.593651500294504 chr20 63025520 140659027 2.2317789206657874 5.679608208704609 chr21 48129895 67784812 1.408372322441177 6.855407568813701 chr22 51304566 49583538 0.9664546816359386 3.6235699043908403 chrMT 16571 1313885 79.28821435037113 41.48028220396443 chrX 155270560 250390176 1.6126056092024141 7.683003994225579 chrY 59373566 116705245 1.9656094936254966 45.396725768552656