BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084349.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,356,025 number of mapped reads = 2,105,975 (89.39%) number of supplementary alignments = 13,279 (0.56%) number of secondary alignments = 0 number of mapped bases = 140,180,993 bp number of sequenced bases = 140,132,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,799 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5633 >>>>>>> ACTG content number of A's = 38,933,673 bp (27.78%) number of C's = 27,037,620 bp (19.29%) number of T's = 43,005,855 bp (30.69%) number of G's = 30,985,776 bp (22.11%) number of N's = 169,269 bp (0.12%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,385,124 number of insertions = 10,199 mapped reads with insertion percentage = 0.48% number of deletions = 28,451 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.0453X std coverageData = 0.3191X There is a 3.86% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% 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% 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 13889197 0.05572382104516402 0.49977680492220855 chr2 243199373 13307297 0.05471764518077109 0.3727463397818028 chr3 198022430 9351596 0.04722493305430097 0.24834378955990338 chr4 191154276 6595229 0.03450212643948389 0.2167706204664344 chr5 180915260 7024772 0.03882907389901769 0.22312202697436403 chr6 171115067 6758349 0.039495931705417854 0.2491913467139962 chr7 159138663 7910250 0.049706651110924566 0.4814859856496559 chr8 146364022 7141335 0.04879160125840215 0.3244189948470027 chr9 141213431 5406196 0.03828386550568267 0.27292410499993386 chr10 135534747 10242260 0.075569256052103 0.42667408015350816 chr11 135006516 7965571 0.059001381829599985 0.3249254461594152 chr12 133851895 5026748 0.03755455236550816 0.21972403207242225 chr13 115169878 3425947 0.02974690135557841 0.1955826475589814 chr14 107349540 3793058 0.035333714518012836 0.2205398206802307 chr15 102531392 3021052 0.029464654103203827 0.19941806441762966 chr16 90354753 3267662 0.0361648047446934 0.23081595915338213 chr17 81195210 4106369 0.05057403016754314 0.2724719154124339 chr18 78077248 3758850 0.04814270605439372 0.42045829382403865 chr19 59128983 3106336 0.05253491337742102 0.3920210864564284 chr20 63025520 3039148 0.048220911148372916 0.2527795249431724 chr21 48129895 1566165 0.0325403784903333 0.21250729304936075 chr22 51304566 1219812 0.023775895502166414 0.17420111089400325 chrMT 16571 14249 0.8598756864401665 1.2211953349977012 chrX 155270560 8946450 0.057618456454333646 0.29908429433451345 chrY 59373566 297095 0.0050038261134593125 0.09735300850295027