BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013315.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 = 2,439,583 number of mapped reads = 2,186,457 (89.62%) number of supplementary alignments = 15,314 (0.63%) number of secondary alignments = 0 number of mapped bases = 143,465,143 bp number of sequenced bases = 143,406,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,836 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3994 >>>>>>> ACTG content number of A's = 39,193,369 bp (27.33%) number of C's = 27,384,672 bp (19.1%) number of T's = 44,269,427 bp (30.87%) number of G's = 32,523,908 bp (22.68%) number of N's = 34,938 bp (0.02%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,111,101 number of insertions = 9,579 mapped reads with insertion percentage = 0.43% number of deletions = 33,681 mapped reads with deletion percentage = 1.53% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.3668X There is a 3.8% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 10506152 0.04215095616552145 0.5427612130130303 chr2 243199373 14672303 0.060330348795759436 0.47701274413283123 chr3 198022430 9058616 0.04574540368987493 0.25040888092792013 chr4 191154276 9035357 0.04726735487727201 0.26181273188385673 chr5 180915260 7803234 0.043131983449046805 0.2452778187727136 chr6 171115067 7669895 0.04482302543235424 0.3029957280360488 chr7 159138663 8893971 0.05588818475872202 0.6111197718771936 chr8 146364022 7929799 0.05417860818282241 0.3969960453572564 chr9 141213431 5148925 0.036462006223756435 0.2999534707726016 chr10 135534747 6782036 0.05003909440285449 0.39173083196334807 chr11 135006516 6050018 0.044812785184383246 0.28303125582771665 chr12 133851895 7028345 0.05250837128603969 0.27413132653168576 chr13 115169878 3617584 0.03141085206324522 0.21063080194185696 chr14 107349540 4702966 0.04380983840266106 0.2581536372655117 chr15 102531392 4119868 0.040181528014366565 0.23968988055474966 chr16 90354753 4752911 0.05260277785276 0.290352301260348 chr17 81195210 3784449 0.04660926426571223 0.2798962754789482 chr18 78077248 3455792 0.044261191173131514 0.5156061556585133 chr19 59128983 2909508 0.04920612282474062 0.45294739593972755 chr20 63025520 3263235 0.05177640739814602 0.27269915814973283 chr21 48129895 2381870 0.0494883689233064 0.2708366723800274 chr22 51304566 1483401 0.028913625348667798 0.19950841562408808 chrMT 16571 346575 20.914549514211576 13.644681289776598 chrX 155270560 7757457 0.04996090050811951 0.2816011667909713 chrY 59373566 310876 0.005235932771833176 0.1075763246422719