BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234076.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 = 4,735,649 number of mapped reads = 4,477,923 (94.56%) number of supplementary alignments = 37,647 (0.79%) number of secondary alignments = 0 number of mapped bases = 289,668,113 bp number of sequenced bases = 289,556,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 544,332 duplication rate = 10.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7643 >>>>>>> ACTG content number of A's = 75,773,693 bp (26.17%) number of C's = 52,867,660 bp (18.26%) number of T's = 93,242,379 bp (32.2%) number of G's = 67,645,068 bp (23.36%) number of N's = 27,973 bp (0.01%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,570,979 number of insertions = 19,753 mapped reads with insertion percentage = 0.44% number of deletions = 63,681 mapped reads with deletion percentage = 1.41% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.0936X std coverageData = 0.9316X There is a 6.88% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% 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 28467690 0.11421311564154538 2.0105206907588276 chr2 243199373 13181475 0.05420028364957997 1.462809426121705 chr3 198022430 33382464 0.1685792059010689 0.5347518988294103 chr4 191154276 6838770 0.03577618111979875 0.35540700987328555 chr5 180915260 19364332 0.10703537114558495 0.43720803596214197 chr6 171115067 18537575 0.10833397271790215 0.6318957995113667 chr7 159138663 16255150 0.10214456809907974 0.9148335496795668 chr8 146364022 17332485 0.11842039295695223 1.164444623311135 chr9 141213431 10808099 0.07653733022038109 0.592668932143427 chr10 135534747 10855229 0.08009185275566272 0.7021272893453522 chr11 135006516 14002572 0.10371774944551565 0.7514627406263091 chr12 133851895 11608124 0.0867236433223452 0.39525587381240634 chr13 115169878 12027549 0.10443311401267613 0.4599886283802194 chr14 107349540 13815213 0.1286937326419843 0.507196914890678 chr15 102531392 7462099 0.07277867640770935 0.37056234720542813 chr16 90354753 5658609 0.06262657815023853 0.42698006980986775 chr17 81195210 9084798 0.11188834907872028 0.5122502144147266 chr18 78077248 5855608 0.07499762286703547 1.5219786006090714 chr19 59128983 9091777 0.1537617685729518 1.0932471742119014 chr20 63025520 6932980 0.11000274174651792 0.4894437366973174 chr21 48129895 7125665 0.14805070736181744 0.5404845482377376 chr22 51304566 3383567 0.06595060174566139 0.3211229529297122 chrMT 16571 241058 14.546979663267154 9.709398659894642 chrX 155270560 7654643 0.04929874021192427 0.40503404798065185 chrY 59373566 700582 0.011799560767497105 0.3104184714174958