BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354853.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 22,132,406 number of mapped reads = 21,165,408 (95.63%) number of supplementary alignments = 189,523 (0.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,638,107 number of mapped paired reads (second in pair) = 10,527,301 number of mapped paired reads (both in pair) = 21,018,094 number of mapped paired reads (singletons) = 147,314 number of mapped bases = 3,059,271,878 bp number of sequenced bases = 3,057,966,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,975,877 duplication rate = 60.79% >>>>>>> Insert size mean insert size = 68,360.8609 std insert size = 2,848,983.1246 median insert size = 404 >>>>>>> Mapping quality mean mapping quality = 54.3202 >>>>>>> ACTG content number of A's = 892,893,749 bp (29.2%) number of C's = 628,726,341 bp (20.56%) number of T's = 896,147,436 bp (29.31%) number of G's = 640,177,333 bp (20.93%) number of N's = 21,339 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 29,864,257 number of insertions = 435,917 mapped reads with insertion percentage = 1.94% number of deletions = 472,294 mapped reads with deletion percentage = 2.14% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.9882X std coverageData = 14.4923X There is a 28.8% of reference with a coverageData >= 1X There is a 21.1% of reference with a coverageData >= 2X There is a 14.34% of reference with a coverageData >= 3X There is a 10.09% of reference with a coverageData >= 4X There is a 6.58% of reference with a coverageData >= 5X There is a 4.54% of reference with a coverageData >= 6X There is a 2.91% of reference with a coverageData >= 7X There is a 2% of reference with a coverageData >= 8X There is a 1.28% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 263960701 1.0590172250764422 32.75328416681277 chr2 243199373 272232659 1.1193805956070455 26.552972044285372 chr3 198022430 209818942 1.059571594995577 2.1637393770557725 chr4 191154276 201616688 1.0547328169629855 11.525324254946101 chr5 180915260 185230710 1.02385343281711 2.1312631533646895 chr6 171115067 178189376 1.0413424084975522 4.539507108303169 chr7 159138663 164518331 1.0338049088674321 10.70107285655639 chr8 146364022 149741942 1.0230788957138661 5.319137782055182 chr9 141213431 131945132 0.9343667317310632 19.68037267378251 chr10 135534747 165404408 1.2203837883727338 17.567265124442862 chr11 135006516 144238404 1.0683810550299662 5.7352242652973455 chr12 133851895 140990989 1.0533357708533002 2.139245936365373 chr13 115169878 97820252 0.849356217951364 1.9176079278209583 chr14 107349540 93149095 0.8677176911983041 2.1502444274242616 chr15 102531392 88644287 0.8645575298538812 1.9432483220149515 chr16 90354753 88330402 0.9775955228387376 4.145321055561198 chr17 81195210 86472770 1.064998415546927 5.352943846461632 chr18 78077248 84117375 1.077360910568979 14.29513900312387 chr19 59128983 57390608 0.9706002892016594 17.99756508193498 chr20 63025520 66343670 1.052647721113606 4.1930666131754535 chr21 48129895 38804681 0.8062490267223729 5.983015958950224 chr22 51304566 37127627 0.7236710081515941 2.7808271050389726 chrMT 16571 7768852 468.8221591937723 94.42313078143225 chrX 155270560 78777456 0.5073560371006584 1.9408015761136872 chrY 59373566 26636521 0.4486259255507746 12.139682683128829