BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 431,922 number of mapped reads = 280,286 (64.89%) number of supplementary alignments = 8,829 (2.04%) number of secondary alignments = 0 number of mapped bases = 36,100,108 bp number of sequenced bases = 35,394,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,082 duplication rate = 42.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.343 >>>>>>> ACTG content number of A's = 9,913,539 bp (28.01%) number of C's = 7,416,737 bp (20.95%) number of T's = 9,392,985 bp (26.54%) number of G's = 8,671,444 bp (24.5%) number of N's = 294 bp (0%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0429 number of mismatches = 1,391,026 number of insertions = 39,100 mapped reads with insertion percentage = 13.35% number of deletions = 119,352 mapped reads with deletion percentage = 40.64% homopolymer indels = 29.21% >>>>>>> Coverage mean coverageData = 0.0117X std coverageData = 1.6875X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 3045834 0.01221996554223229 1.2804991819135774 chr2 243199373 3941790 0.016208059878509637 4.189110461096114 chr3 198022430 1858594 0.009385775136685273 0.8877541045776757 chr4 191154276 1854742 0.009702853835192262 1.109305163346593 chr5 180915260 1955057 0.010806479232321253 1.0917833060476896 chr6 171115067 1464740 0.008559970934645982 0.8546655372243246 chr7 159138663 1472528 0.009253112802638037 0.9547656709006068 chr8 146364022 1858375 0.012696938596016444 1.720115825486291 chr9 141213431 1309419 0.009272623650083255 1.0664014523185958 chr10 135534747 2014698 0.014864808062835725 1.4070167635825686 chr11 135006516 1821645 0.013493015403789844 1.58250691146485 chr12 133851895 1371539 0.010246690941506655 1.1112762941865737 chr13 115169878 1000779 0.008689589824867228 1.0775493267363399 chr14 107349540 1171857 0.01091627407066672 1.1222309024748216 chr15 102531392 936693 0.009135670371080108 0.9021439184366221 chr16 90354753 1209621 0.013387463966616123 1.5020638416525838 chr17 81195210 1320534 0.016263693387824234 1.78874624439189 chr18 78077248 966210 0.012375051948552285 1.3812119685076674 chr19 59128983 644216 0.010895096910427159 1.0648131222766914 chr20 63025520 858637 0.013623640074687205 1.1076917204504464 chr21 48129895 289427 0.006013455878098217 0.5210007464430793 chr22 51304566 374074 0.007291241875040907 0.8684415805165377 chrMT 16571 301988 18.223885100476735 168.3657615680324 chrX 155270560 2920619 0.01880986968811087 1.2665464349499485 chrY 59373566 136492 0.0022988681528746313 0.4247030215777968