BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081154.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 = 2,914,230 number of mapped reads = 2,630,994 (90.28%) number of supplementary alignments = 24,068 (0.83%) number of secondary alignments = 0 number of mapped bases = 176,674,510 bp number of sequenced bases = 176,606,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,270 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8728 >>>>>>> ACTG content number of A's = 49,788,244 bp (28.19%) number of C's = 32,711,036 bp (18.52%) number of T's = 55,133,050 bp (31.22%) number of G's = 38,921,800 bp (22.04%) number of N's = 52,362 bp (0.03%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,486,588 number of insertions = 13,926 mapped reads with insertion percentage = 0.53% number of deletions = 41,498 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.4998X There is a 4.88% of reference with a coverageData >= 1X There is a 0.6% 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 0.01% 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 14021166 0.056253284119199845 0.941105948116863 chr2 243199373 14962477 0.061523501542909 0.6075824638937212 chr3 198022430 12170866 0.06146205760630248 0.2784308108586771 chr4 191154276 12203176 0.06383940895991257 0.30433604211968396 chr5 180915260 11225198 0.06204671734158854 0.28491121924454493 chr6 171115067 10513475 0.061440965920318405 0.4182732878081428 chr7 159138663 9210219 0.0578754328230092 0.5675790037494157 chr8 146364022 9122362 0.06232653267754558 0.6649432559757089 chr9 141213431 7426771 0.05259252570670845 0.48513821265858864 chr10 135534747 8089159 0.059683285497260714 0.404491602704301 chr11 135006516 8232025 0.06097501990200236 0.45035753824814 chr12 133851895 7919455 0.05916580411506314 0.28440449139586543 chr13 115169878 5647114 0.04903290771915205 0.24957199775896707 chr14 107349540 5714379 0.053231518271992594 0.3018413321789097 chr15 102531392 4950057 0.048278453100490434 0.2626948371575875 chr16 90354753 4632280 0.051267695900845414 0.3203884417363791 chr17 81195210 4338713 0.05343557828103407 0.31609986814044155 chr18 78077248 4961377 0.06354446560411556 0.9929604188354084 chr19 59128983 3107147 0.05254862915535009 0.6598677479031744 chr20 63025520 3263538 0.051781214974505566 0.2757647463534985 chr21 48129895 2329709 0.04840461422157684 0.2831704848803516 chr22 51304566 1726241 0.03364692725399918 0.20471584759667272 chrMT 16571 5634 0.33999155150564236 0.6873885518710148 chrX 155270560 10463703 0.06739012856010825 0.3493638140153426 chrY 59373566 438269 0.0073815509076884485 0.15186337949454506