BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238314.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 = 3,286,916 number of mapped reads = 2,787,323 (84.8%) number of supplementary alignments = 27,556 (0.84%) number of secondary alignments = 0 number of mapped bases = 178,065,780 bp number of sequenced bases = 177,960,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,681 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6392 >>>>>>> ACTG content number of A's = 48,135,633 bp (27.05%) number of C's = 33,154,747 bp (18.63%) number of T's = 55,547,167 bp (31.21%) number of G's = 41,076,595 bp (23.08%) number of N's = 46,374 bp (0.03%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,632,314 number of insertions = 13,915 mapped reads with insertion percentage = 0.49% number of deletions = 62,828 mapped reads with deletion percentage = 2.23% homopolymer indels = 43.62% >>>>>>> Coverage mean coverageData = 0.0575X std coverageData = 0.5385X There is a 4.53% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11708790 0.046975971225363566 0.835894171108904 chr2 243199373 16916165 0.06955677883264938 0.6935040467905286 chr3 198022430 4616589 0.02331346504534865 0.18441604157947045 chr4 191154276 4708231 0.02463052932177149 0.25878765895069167 chr5 180915260 7450511 0.04118232480775806 0.24874205605798777 chr6 171115067 7152373 0.04179861613238301 0.4226447622622656 chr7 159138663 13154758 0.0826622377743616 0.7510945843049488 chr8 146364022 7344835 0.050181970265889525 0.7353567489428483 chr9 141213431 11353375 0.0803986909715408 0.5399122588360123 chr10 135534747 6865422 0.0506543314682249 0.46484773325023654 chr11 135006516 12866795 0.09530499253828607 0.5453466801358823 chr12 133851895 10550494 0.07882214891317003 0.35402065463047305 chr13 115169878 9501931 0.08250361261995953 0.34820556924277984 chr14 107349540 12504298 0.11648208273645141 0.46731495875052337 chr15 102531392 3512375 0.03425658163306707 0.23110144683692396 chr16 90354753 3930372 0.043499338656816426 0.3308480514399371 chr17 81195210 3330408 0.0410172964636707 0.3603894241417692 chr18 78077248 5663048 0.07253134741634336 1.1877369895614145 chr19 59128983 1953957 0.0330456723735634 0.5786713726575956 chr20 63025520 5010348 0.07949713068610938 0.374815334480579 chr21 48129895 2963883 0.0615809155619392 0.3519219442512756 chr22 51304566 2662042 0.05188703867020335 0.276411356212006 chrMT 16571 21863 1.3193530867177599 1.559104987190947 chrX 155270560 11751733 0.07568551952153711 0.4564767737055293 chrY 59373566 571184 0.009620173395008817 0.21912411101482893