BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716588.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,517,451 number of mapped reads = 2,114,967 (84.01%) number of supplementary alignments = 9,534 (0.38%) number of secondary alignments = 0 number of mapped bases = 119,667,383 bp number of sequenced bases = 119,632,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,281 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8243 >>>>>>> ACTG content number of A's = 29,865,721 bp (24.96%) number of C's = 23,181,245 bp (19.38%) number of T's = 37,619,949 bp (31.45%) number of G's = 28,964,530 bp (24.21%) number of N's = 891 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 630,643 number of insertions = 8,317 mapped reads with insertion percentage = 0.39% number of deletions = 21,721 mapped reads with deletion percentage = 1.02% homopolymer indels = 39.22% >>>>>>> Coverage mean coverageData = 0.0387X std coverageData = 0.3076X There is a 3.42% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 10052141 0.040329452178175317 0.38782525389951317 chr2 243199373 9243093 0.03800623696509283 0.49386675761824017 chr3 198022430 6667290 0.03366936765698714 0.2095766456580844 chr4 191154276 6921736 0.03621020750799213 0.23361424597447158 chr5 180915260 6584693 0.036396559361548605 0.21046677305312897 chr6 171115067 6242140 0.0364791956046746 0.2594056893295662 chr7 159138663 6733799 0.04231403527626721 0.4260711064567063 chr8 146364022 6051740 0.041347182984627195 0.2804875610088567 chr9 141213431 4047136 0.02865971013762848 0.22711865365913225 chr10 135534747 5298312 0.039091909029055114 0.4178508607086872 chr11 135006516 4348461 0.03220926758823996 0.253054381259358 chr12 133851895 6061590 0.04528579890482686 0.23821103651028763 chr13 115169878 3400786 0.029528432773020738 0.19001945614578425 chr14 107349540 4241652 0.039512530747686486 0.23040638123574889 chr15 102531392 4362532 0.04254825683045442 0.23438289135354812 chr16 90354753 4481610 0.049600157724962186 0.2743794219063591 chr17 81195210 5851113 0.07206229283722525 0.3177776463550692 chr18 78077248 2115502 0.027094986749532975 0.3521957368065347 chr19 59128983 3638088 0.06152799888339023 0.386416120939514 chr20 63025520 4165775 0.06609663831413053 0.3086272214730905 chr21 48129895 1483269 0.030818039391110243 0.2124881532999087 chr22 51304566 1270007 0.024754268460238024 0.17580063144970337 chrMT 16571 9120 0.5503590610101985 0.8949676620689918 chrX 155270560 6024891 0.03880253281755408 0.2382983992942109 chrY 59373566 370907 0.006247005611891326 0.1766201251554683