BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927011.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,002,494 number of mapped reads = 10,767,459 (97.86%) number of supplementary alignments = 309,776 (2.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,406,334 number of mapped paired reads (second in pair) = 5,361,125 number of mapped paired reads (both in pair) = 10,638,008 number of mapped paired reads (singletons) = 129,451 number of mapped bases = 985,291,469 bp number of sequenced bases = 984,532,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 597,435 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 327,912.545 std insert size = 5,565,370.4923 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 52.5272 >>>>>>> ACTG content number of A's = 281,884,124 bp (28.63%) number of C's = 191,487,734 bp (19.45%) number of T's = 286,799,215 bp (29.13%) number of G's = 224,171,603 bp (22.77%) number of N's = 189,597 bp (0.02%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 9,388,763 number of insertions = 172,698 mapped reads with insertion percentage = 1.57% number of deletions = 512,324 mapped reads with deletion percentage = 4.63% homopolymer indels = 51.74% >>>>>>> Coverage mean coverageData = 0.3183X std coverageData = 1.4252X There is a 19.37% of reference with a coverageData >= 1X There is a 7.12% of reference with a coverageData >= 2X There is a 2.66% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 82880173 0.3325174182815777 1.8943244490678017 chr2 243199373 88790567 0.36509373319807037 2.542695913665756 chr3 198022430 66374603 0.3351872967117917 0.8225992995521454 chr4 191154276 58832771 0.3077763795354492 1.0399351597193205 chr5 180915260 49922195 0.2759424218830407 0.7288433649000345 chr6 171115067 64134410 0.37480282200982334 1.1323610069591563 chr7 159138663 51924385 0.326283908769549 1.077011158281222 chr8 146364022 48232306 0.32953662615256635 0.9254058316456789 chr9 141213431 43935790 0.3111303909895086 1.6591905934595212 chr10 135534747 47272818 0.3487874441526054 2.5459107908281955 chr11 135006516 48508192 0.3593025984019912 1.0981502522389268 chr12 133851895 44320846 0.33111855457855116 0.8238605747893721 chr13 115169878 25442269 0.22091079231672017 0.645755556638052 chr14 107349540 28749266 0.2678098667213665 0.7506405153875597 chr15 102531392 29648808 0.28916810180437225 0.7784463100560514 chr16 90354753 37441609 0.4143844984004328 2.1434873169338258 chr17 81195210 23500974 0.28943793605558754 0.9422504680370488 chr18 78077248 28572934 0.36595723763214605 1.599305693183742 chr19 59128983 15493046 0.26202118172741107 1.1908220894673773 chr20 63025520 22430161 0.35589013783622886 0.9012130459740216 chr21 48129895 12386849 0.2573628926470752 1.2188147654048784 chr22 51304566 11319484 0.22063307191800433 0.7192215362172606 chrMT 16571 53866 3.2506185504797536 3.3807318843557783 chrX 155270560 53192282 0.3425780263818202 0.9231333132308503 chrY 59373566 1930865 0.03252061700319634 1.301248064695491