BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548926.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,438,433 number of mapped reads = 5,605,462 (87.06%) number of secondary alignments = 0 number of mapped bases = 222,048,861 bp number of sequenced bases = 222,024,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,884 duplication rate = 2.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.704 >>>>>>> ACTG content number of A's = 65,371,386 bp (29.44%) number of C's = 45,557,140 bp (20.52%) number of T's = 65,637,537 bp (29.56%) number of G's = 45,456,118 bp (20.47%) number of N's = 2,046 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 589,908 number of insertions = 6,854 mapped reads with insertion percentage = 0.12% number of deletions = 18,477 mapped reads with deletion percentage = 0.33% homopolymer indels = 41.59% >>>>>>> Coverage mean coverageData = 0.0717X std coverageData = 0.818X There is a 6.04% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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 17716645 0.07107964236526415 0.7613161468546227 chr2 243199373 18891447 0.077678847469726 0.41250025661791595 chr3 198022430 15095582 0.0762316773912935 0.3168049325020913 chr4 191154276 14717240 0.07699142445550107 0.3256450103345302 chr5 180915260 13935024 0.07702514425814605 0.3221199069018894 chr6 171115067 13014003 0.07605410340633534 0.347165502077117 chr7 159138663 12166299 0.07645093134909647 0.57417545501903 chr8 146364022 11760667 0.08035217151930958 3.2259892003674784 chr9 141213431 9275074 0.06568124529174565 0.38933127886120056 chr10 135534747 10164712 0.07499709281192667 0.3893378578681529 chr11 135006516 10025216 0.07425727510811404 0.44197114440935087 chr12 133851895 10041976 0.07502303945715524 0.32157265578843286 chr13 115169878 7211543 0.06261657236452052 0.2835138926273674 chr14 107349540 6838340 0.06370162368651044 0.3270362318148423 chr15 102531392 6466340 0.06306692880947135 0.2875667933537971 chr16 90354753 6020653 0.06663349519642868 0.31506138813593015 chr17 81195210 5611186 0.06910735251500673 0.31956005802017867 chr18 78077248 5897358 0.07553234970576832 0.6747131331210359 chr19 59128983 4105336 0.0694301811346899 0.6766917412639475 chr20 63025520 4401498 0.06983675818938107 0.3110302076627417 chr21 48129895 2805223 0.05828441969383062 0.3000546736635319 chr22 51304566 2366381 0.046124179278702014 0.28252141016496035 chrMT 16571 9319 0.5623679922756623 1.0724830173856361 chrX 155270560 12878615 0.08294305758928157 0.3829827897562977 chrY 59373566 633184 0.01066440914126667 0.15196008613876918