BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004097.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 = 3,989,520 number of mapped reads = 3,227,576 (80.9%) number of supplementary alignments = 29,998 (0.75%) number of secondary alignments = 0 number of mapped bases = 213,366,534 bp number of sequenced bases = 213,266,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,902 duplication rate = 6.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9309 >>>>>>> ACTG content number of A's = 59,077,262 bp (27.7%) number of C's = 38,991,983 bp (18.28%) number of T's = 68,981,295 bp (32.35%) number of G's = 46,187,426 bp (21.66%) number of N's = 28,244 bp (0.01%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 2,015,116 number of insertions = 17,297 mapped reads with insertion percentage = 0.53% number of deletions = 60,927 mapped reads with deletion percentage = 1.86% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.0689X std coverageData = 0.5393X There is a 4.52% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 19402799 0.07784453624290068 0.9792583288269144 chr2 243199373 17372493 0.07143313235433382 0.6047874040801361 chr3 198022430 14550063 0.0734768430020781 0.3890090484977419 chr4 191154276 14772345 0.07727969946118286 0.4155797428372498 chr5 180915260 11194372 0.061876328177070304 0.355233492662916 chr6 171115067 12307380 0.07192458394093373 0.4494760650989479 chr7 159138663 10954925 0.06883886538621982 0.68607119672002 chr8 146364022 12869945 0.08793106956298317 0.6572428672211033 chr9 141213431 8284949 0.05866969551925978 0.46224000352614075 chr10 135534747 11082346 0.08176756326552924 0.5513234733907855 chr11 135006516 7245767 0.053669757687843746 0.4058539347164787 chr12 133851895 7384085 0.05516608487313534 0.33555274096924204 chr13 115169878 8032601 0.06974567603518692 0.37977951332097676 chr14 107349540 6675898 0.062188417388653924 0.37061844941910016 chr15 102531392 6475997 0.0631611145979565 0.36502308151826646 chr16 90354753 6015542 0.06657692927343845 0.3862754148961927 chr17 81195210 4778344 0.058850072559699027 0.3861979112265972 chr18 78077248 5809079 0.07440168741603187 0.8058201599663107 chr19 59128983 3762155 0.06362624231165959 0.6606164600789713 chr20 63025520 4002182 0.06350097547786991 0.3688623584424845 chr21 48129895 3411741 0.07088610935053982 0.40169932182356904 chr22 51304566 1752811 0.034164814882168576 0.2545533812008203 chrMT 16571 99183 5.985335827650715 4.887321885186633 chrX 155270560 14580568 0.0939042662047461 0.47514152836080126 chrY 59373566 548964 0.00924593277755963 0.17323675778610226