BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013276.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 = 2,705,987 number of mapped reads = 2,431,456 (89.85%) number of supplementary alignments = 19,357 (0.72%) number of secondary alignments = 0 number of mapped bases = 156,821,027 bp number of sequenced bases = 156,758,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,186 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0098 >>>>>>> ACTG content number of A's = 42,686,403 bp (27.23%) number of C's = 31,057,309 bp (19.81%) number of T's = 46,539,986 bp (29.69%) number of G's = 36,439,503 bp (23.25%) number of N's = 35,221 bp (0.02%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,261,420 number of insertions = 11,049 mapped reads with insertion percentage = 0.45% number of deletions = 35,810 mapped reads with deletion percentage = 1.46% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.4275X There is a 4.48% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 11603224 0.04655243767677514 0.6541643810855606 chr2 243199373 15757327 0.06479180766637914 0.5543365534770368 chr3 198022430 9692897 0.048948480230244625 0.2409791301944298 chr4 191154276 9329227 0.048804699508788386 0.25465133317694877 chr5 180915260 8248237 0.04559171514884924 0.23644889012852052 chr6 171115067 8101328 0.04734432883107833 0.30541078210404454 chr7 159138663 9808578 0.06163541791223921 0.8119169655209258 chr8 146364022 8549320 0.058411349204383026 0.3636928867067079 chr9 141213431 5673795 0.04017886230665977 0.3632519437000502 chr10 135534747 7468556 0.05510436375404161 0.4378002058062191 chr11 135006516 6599707 0.04888435903345584 0.3335634320687321 chr12 133851895 7849040 0.058639737599531186 0.26846456664043233 chr13 115169878 3745533 0.03252181095477066 0.20130843502731932 chr14 107349540 5277379 0.04916070436817894 0.27234461210568894 chr15 102531392 4410868 0.043019683181517714 0.2317789807363181 chr16 90354753 5482539 0.06067792581979611 0.3070121114959421 chr17 81195210 4447305 0.054772997077044326 0.29236569884094427 chr18 78077248 3700752 0.04739859683579011 0.6625787205026156 chr19 59128983 3637518 0.06151835894082602 0.55076269860626 chr20 63025520 3822776 0.060654414275360204 0.27728589868386494 chr21 48129895 2591754 0.05384915134346335 0.2746731823068882 chr22 51304566 1738857 0.0338928312930276 0.20013133607833467 chrMT 16571 580241 35.015448675396776 24.110991371635166 chrX 155270560 8324843 0.053615076805287494 0.290587981355552 chrY 59373566 379426 0.006390486971929562 0.1342513026761869