BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524522.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 = 2,468,436 number of mapped reads = 2,267,786 (91.87%) number of supplementary alignments = 10,296 (0.42%) number of secondary alignments = 0 number of mapped bases = 131,271,239 bp number of sequenced bases = 131,237,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,304 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3734 >>>>>>> ACTG content number of A's = 32,937,355 bp (25.1%) number of C's = 25,902,296 bp (19.74%) number of T's = 40,512,552 bp (30.87%) number of G's = 31,881,449 bp (24.29%) number of N's = 3,932 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 619,456 number of insertions = 7,914 mapped reads with insertion percentage = 0.35% number of deletions = 20,250 mapped reads with deletion percentage = 0.89% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.3377X There is a 3.63% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 9415112 0.03777367519577815 0.566202381637826 chr2 243199373 11562190 0.04754202224032872 0.35530138687771623 chr3 198022430 7616138 0.03846098646501813 0.21903538452362084 chr4 191154276 8017811 0.041944188577816593 0.26767556635407513 chr5 180915260 6854986 0.03789059032388976 0.22129882304435627 chr6 171115067 6994449 0.040875705001477164 0.24185235854450962 chr7 159138663 8046732 0.050564280535648334 0.4348349010141242 chr8 146364022 5562879 0.038007147685515226 0.34893470160605977 chr9 141213431 6188254 0.043821993107723584 0.3388513655526071 chr10 135534747 5400299 0.039844387653595575 0.3389968334238897 chr11 135006516 4774405 0.03536425604820437 0.28819593320295495 chr12 133851895 10399725 0.0776957621705692 0.3708753205016618 chr13 115169878 4774696 0.0414578541100825 0.2288873444862465 chr14 107349540 5102249 0.047529304736657466 0.26913922970956256 chr15 102531392 3632330 0.03542651600789737 0.2098987169757724 chr16 90354753 3672333 0.04064349553365499 0.24291522731257428 chr17 81195210 4515220 0.05560943804443637 0.2800582639372463 chr18 78077248 2507209 0.0321119028170665 0.5909221806038071 chr19 59128983 2309271 0.039054806675771846 0.42700437437862093 chr20 63025520 4045944 0.06419532913016822 0.29870236252202675 chr21 48129895 1689382 0.03510047133907107 0.24183553625451176 chr22 51304566 1315854 0.025647892626165087 0.17782552322384845 chrMT 16571 41491 2.50383199565506 2.3980832407383805 chrX 155270560 6472951 0.04168820541382732 0.2671349029374408 chrY 59373566 359329 0.006052003007533689 0.1429156837324606