BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716361.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 = 2,942,396 number of mapped reads = 2,643,212 (89.83%) number of supplementary alignments = 13,911 (0.47%) number of secondary alignments = 0 number of mapped bases = 152,391,052 bp number of sequenced bases = 152,347,870 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,666 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1442 >>>>>>> ACTG content number of A's = 38,674,204 bp (25.39%) number of C's = 30,018,317 bp (19.7%) number of T's = 47,410,997 bp (31.12%) number of G's = 36,243,263 bp (23.79%) number of N's = 1,089 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 768,957 number of insertions = 11,477 mapped reads with insertion percentage = 0.43% number of deletions = 27,660 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.02% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.4085X There is a 4.26% of reference with a coverageData >= 1X There is a 0.48% 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 17808782 0.0714492984151883 0.6841263842578901 chr2 243199373 15544944 0.06391852005309241 0.6037400647982669 chr3 198022430 9577020 0.04836330914634267 0.250891030543852 chr4 191154276 6389364 0.03342516910267809 0.22682109134483278 chr5 180915260 10917502 0.06034594317803816 0.27940467440673633 chr6 171115067 5497076 0.03212502613811325 0.24569673019098467 chr7 159138663 10116659 0.06357134595255459 0.7170254014407959 chr8 146364022 6698641 0.0457669918362861 0.319602926342584 chr9 141213431 4163496 0.029483711078445506 0.2999558994903329 chr10 135534747 6775982 0.04999442689039734 0.3491685657635082 chr11 135006516 6491124 0.04808007933483744 0.38262877143335244 chr12 133851895 6049343 0.04519430225474208 0.2432766439491438 chr13 115169878 4459690 0.03872271185352823 0.2254918918642097 chr14 107349540 3251271 0.03028677160610097 0.2136451956938652 chr15 102531392 6561488 0.06399491777113492 0.29856271297544734 chr16 90354753 4426570 0.04899100327350792 0.27513424204159354 chr17 81195210 5700385 0.07020592717230487 0.3380472338898822 chr18 78077248 4864817 0.06230774168679716 0.6807741937226688 chr19 59128983 2371260 0.040103175797899314 0.5023466275781288 chr20 63025520 3905634 0.06196908807733756 0.28478861202606337 chr21 48129895 1899642 0.03946906595162944 0.23210719007721728 chr22 51304566 1736536 0.03384759165490261 0.20747268685692533 chrMT 16571 15336 0.9254722104882023 1.0775931727241435 chrX 155270560 6818424 0.04391317967810511 0.28012353779355725 chrY 59373566 350066 0.005895990818540358 0.1260727596788371