BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525133.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 = 1,778,592 number of mapped reads = 1,561,456 (87.79%) number of supplementary alignments = 43,204 (2.43%) number of secondary alignments = 0 number of mapped bases = 119,560,771 bp number of sequenced bases = 119,511,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,733 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.947 >>>>>>> ACTG content number of A's = 32,084,161 bp (26.85%) number of C's = 22,786,774 bp (19.07%) number of T's = 37,481,782 bp (31.36%) number of G's = 27,154,114 bp (22.72%) number of N's = 4,371 bp (0%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 904,202 number of insertions = 10,967 mapped reads with insertion percentage = 0.69% number of deletions = 28,699 mapped reads with deletion percentage = 1.81% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3935X There is a 3.4% of reference with a coverageData >= 1X There is a 0.31% 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% 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 9416890 0.03778080857820611 0.5916139378658415 chr2 243199373 10366531 0.04262564854556595 0.5987380707973432 chr3 198022430 7981724 0.04030717126337658 0.22076521470629556 chr4 191154276 7924839 0.041457817035701575 0.239184967857383 chr5 180915260 7384142 0.04081547349847658 0.22692367557206897 chr6 171115067 6996553 0.040888000821108286 0.26092972968673006 chr7 159138663 6703233 0.042121963787015104 0.587306327921654 chr8 146364022 6297737 0.04302790340101476 0.541937051818559 chr9 141213431 5015287 0.03551565148218798 0.39598048850321244 chr10 135534747 5573477 0.04112212641677783 0.39389605761676105 chr11 135006516 5395097 0.039961752660886384 0.3706177348772021 chr12 133851895 5433782 0.04059548054960298 0.22475059298510408 chr13 115169878 3837112 0.033316975468186225 0.19972234453084206 chr14 107349540 3603357 0.03356658072312187 0.24481412363157573 chr15 102531392 3360936 0.032779580325994206 0.19962010446268083 chr16 90354753 3314482 0.03668298445793992 0.24332217419176158 chr17 81195210 3019031 0.03718237812304445 0.26562447963412394 chr18 78077248 3294838 0.04219971994914575 0.6704801687305828 chr19 59128983 2231750 0.03774375757485969 0.4681326234510396 chr20 63025520 2326442 0.036912698221291944 0.2172777286514089 chr21 48129895 1589080 0.03301648590756327 0.21741683297342185 chr22 51304566 1200279 0.023395169155119643 0.16635701127222116 chrMT 16571 13046 0.787278981352966 1.098407130712374 chrX 155270560 7008198 0.045135394629864156 0.3132925851127644 chrY 59373566 272928 0.004596793125075223 0.10918788557069334