BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174047.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 = 5,310,928 number of mapped reads = 5,173,257 (97.41%) number of supplementary alignments = 492,281 (9.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,586,453 number of mapped paired reads (second in pair) = 2,586,804 number of mapped paired reads (both in pair) = 5,077,244 number of mapped paired reads (singletons) = 96,013 number of mapped bases = 613,465,439 bp number of sequenced bases = 613,153,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,904,400 duplication rate = 64.88% >>>>>>> Insert size mean insert size = 915,521.3768 std insert size = 8,949,734.3565 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.8527 >>>>>>> ACTG content number of A's = 183,872,064 bp (29.99%) number of C's = 120,550,002 bp (19.66%) number of T's = 183,759,184 bp (29.97%) number of G's = 124,965,346 bp (20.38%) number of N's = 6,990 bp (0%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 5,993,566 number of insertions = 61,278 mapped reads with insertion percentage = 1.15% number of deletions = 130,177 mapped reads with deletion percentage = 2.45% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.1982X std coverageData = 2.8478X There is a 4.41% of reference with a coverageData >= 1X There is a 3.47% of reference with a coverageData >= 2X There is a 2.63% of reference with a coverageData >= 3X There is a 2.12% of reference with a coverageData >= 4X There is a 1.56% of reference with a coverageData >= 5X There is a 1.24% of reference with a coverageData >= 6X There is a 0.89% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.51% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 45390031 0.18210598961757452 1.785004675494664 chr2 243199373 52941330 0.2176869510268022 8.71406404387898 chr3 198022430 47453518 0.23963708555641905 1.3723702979011074 chr4 191154276 33400115 0.1747285789202016 1.2882629473317981 chr5 180915260 41859419 0.23137583308340048 1.3219097728246911 chr6 171115067 29976383 0.1751826038790611 1.2951658049488786 chr7 159138663 37519938 0.23576884015922642 1.7688428685252182 chr8 146364022 38455416 0.2627381748227717 1.9213792429835623 chr9 141213431 23887041 0.16915558832360642 1.3882215029402283 chr10 135534747 26431301 0.19501494328978236 2.381533871424344 chr11 135006516 21579768 0.15984241827261136 1.1246538747298447 chr12 133851895 29046485 0.21700466026274787 1.279852423118055 chr13 115169878 15050688 0.13068250363172218 0.9980893388363269 chr14 107349540 15682477 0.14608797578452595 1.0516297043054978 chr15 102531392 22150875 0.21603993243357117 1.2726200668175252 chr16 90354753 20119325 0.22267035581404335 1.6916391513965445 chr17 81195210 25063485 0.3086818175604201 1.6939520534257406 chr18 78077248 12603445 0.16142276172438866 2.0419639115628967 chr19 59128983 8098529 0.1369637796746817 1.4177356095120486 chr20 63025520 28562921 0.4531961180169557 2.0614866636780254 chr21 48129895 8415263 0.17484482357586692 1.2113274044505113 chr22 51304566 4723607 0.09206991440099113 0.8084617671233024 chrMT 16571 1266265 76.41451934101744 66.64834638413394 chrX 155270560 22754660 0.14654845065284752 1.0503964465714806 chrY 59373566 1033154 0.017400908680472383 0.6006661519964844