BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063577.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,372,915 number of mapped reads = 1,819,436 (76.68%) number of supplementary alignments = 13,919 (0.59%) number of secondary alignments = 0 number of mapped bases = 119,794,285 bp number of sequenced bases = 119,737,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 281,598 duplication rate = 11.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9392 >>>>>>> ACTG content number of A's = 33,150,825 bp (27.69%) number of C's = 21,751,885 bp (18.17%) number of T's = 38,525,207 bp (32.17%) number of G's = 26,306,310 bp (21.97%) number of N's = 3,044 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 929,876 number of insertions = 8,777 mapped reads with insertion percentage = 0.48% number of deletions = 32,378 mapped reads with deletion percentage = 1.76% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 0.0387X std coverageData = 0.4292X There is a 1.75% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 9430116 0.03783387163556957 0.5210912777890913 chr2 243199373 11632985 0.047833120852659436 0.48931272425517286 chr3 198022430 7462879 0.03768703878646475 0.3648037488369185 chr4 191154276 7475257 0.03910588429630525 0.37613347374579675 chr5 180915260 6400802 0.035380111108371956 0.3550342223423143 chr6 171115067 7157870 0.04183074071437555 0.410063531001613 chr7 159138663 6693279 0.04205941456225506 0.5605813181290394 chr8 146364022 6489144 0.0443356496448287 0.5747243849871585 chr9 141213431 4389338 0.031083006544894445 0.37948683531057753 chr10 135534747 5956607 0.043948929199683386 0.44794542730213494 chr11 135006516 6953871 0.05150766945204334 0.4718300071979096 chr12 133851895 5622126 0.0420025880096804 0.38760558796728944 chr13 115169878 3275345 0.028439250408861246 0.331240000796334 chr14 107349540 3984178 0.037114066813886674 0.3704589754008743 chr15 102531392 3796026 0.03702306119085948 0.36551950481384926 chr16 90354753 3182129 0.0352181694304449 0.350904499605176 chr17 81195210 2894601 0.035649898559286936 0.36405971229695705 chr18 78077248 2786528 0.035689372658216645 0.5664016377084382 chr19 59128983 1984194 0.033557045958324705 0.41535434833557267 chr20 63025520 2473561 0.03924697487620887 0.3769329308966133 chr21 48129895 1723202 0.035803153113049595 0.36041649450963026 chr22 51304566 1255904 0.024479380646159253 0.2944182201882063 chrMT 16571 26988 1.6286283265946533 2.5201749845035843 chrX 155270560 6479850 0.04173263753283301 0.3949053850117289 chrY 59373566 267505 0.004505456182301733 0.12137566291908333