BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777267.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 68,870,482 number of mapped reads = 68,577,783 (99.58%) number of supplementary alignments = 2,309,261 (3.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 34,290,042 number of mapped paired reads (second in pair) = 34,287,741 number of mapped paired reads (both in pair) = 68,476,258 number of mapped paired reads (singletons) = 101,525 number of mapped bases = 6,881,493,738 bp number of sequenced bases = 6,880,469,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,557,781 duplication rate = 48.97% >>>>>>> Insert size mean insert size = 331,562.856 std insert size = 5,665,890.5561 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 54.7035 >>>>>>> ACTG content number of A's = 1,893,813,795 bp (27.52%) number of C's = 1,553,217,373 bp (22.57%) number of T's = 1,884,736,391 bp (27.39%) number of G's = 1,548,616,750 bp (22.51%) number of N's = 85,119 bp (0%) GC percentage = 45.08% >>>>>>> Mismatches and indels general error rate = 0.0022 number of mismatches = 13,846,329 number of insertions = 1,188,533 mapped reads with insertion percentage = 1.71% number of deletions = 470,542 mapped reads with deletion percentage = 0.68% homopolymer indels = 52.19% >>>>>>> Coverage mean coverageData = 2.2229X std coverageData = 20.5777X There is a 20.12% of reference with a coverageData >= 1X There is a 11.79% of reference with a coverageData >= 2X There is a 7.55% of reference with a coverageData >= 3X There is a 5.55% of reference with a coverageData >= 4X There is a 4.41% of reference with a coverageData >= 5X There is a 3.77% of reference with a coverageData >= 6X There is a 3.33% of reference with a coverageData >= 7X There is a 3.04% of reference with a coverageData >= 8X There is a 2.82% of reference with a coverageData >= 9X There is a 2.65% of reference with a coverageData >= 10X There is a 2.51% of reference with a coverageData >= 11X There is a 2.39% of reference with a coverageData >= 12X There is a 2.29% of reference with a coverageData >= 13X There is a 2.2% of reference with a coverageData >= 14X There is a 2.12% of reference with a coverageData >= 15X There is a 2.05% of reference with a coverageData >= 16X There is a 1.98% of reference with a coverageData >= 17X There is a 1.92% of reference with a coverageData >= 18X There is a 1.86% of reference with a coverageData >= 19X There is a 1.81% of reference with a coverageData >= 20X There is a 1.76% of reference with a coverageData >= 21X There is a 1.71% of reference with a coverageData >= 22X There is a 1.67% of reference with a coverageData >= 23X There is a 1.63% of reference with a coverageData >= 24X There is a 1.59% of reference with a coverageData >= 25X There is a 1.55% of reference with a coverageData >= 26X There is a 1.51% of reference with a coverageData >= 27X There is a 1.48% of reference with a coverageData >= 28X There is a 1.45% of reference with a coverageData >= 29X There is a 1.42% of reference with a coverageData >= 30X There is a 1.39% of reference with a coverageData >= 31X There is a 1.36% of reference with a coverageData >= 32X There is a 1.33% of reference with a coverageData >= 33X There is a 1.3% of reference with a coverageData >= 34X There is a 1.28% of reference with a coverageData >= 35X There is a 1.25% of reference with a coverageData >= 36X There is a 1.23% of reference with a coverageData >= 37X There is a 1.21% of reference with a coverageData >= 38X There is a 1.18% of reference with a coverageData >= 39X There is a 1.16% of reference with a coverageData >= 40X There is a 1.14% of reference with a coverageData >= 41X There is a 1.12% of reference with a coverageData >= 42X There is a 1.1% of reference with a coverageData >= 43X There is a 1.08% of reference with a coverageData >= 44X There is a 1.06% of reference with a coverageData >= 45X There is a 1.04% of reference with a coverageData >= 46X There is a 1.03% of reference with a coverageData >= 47X There is a 1.01% of reference with a coverageData >= 48X There is a 0.99% of reference with a coverageData >= 49X There is a 0.98% of reference with a coverageData >= 50X There is a 0.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 678391338 2.7217237625257513 22.30104528105695 chr2 243199373 596035193 2.450808921287803 21.267982844204866 chr3 198022430 417198237 2.1068231361467484 19.476296714492133 chr4 191154276 292988465 1.5327329899750712 16.24399981177711 chr5 180915260 360105162 1.9904631704368112 19.156849868638506 chr6 171115067 324340807 1.895454402036964 19.30638424234887 chr7 159138663 433286500 2.7226978776364357 23.508806810603634 chr8 146364022 223921139 1.529891949812639 17.037565808167344 chr9 141213431 241138989 1.707620778649589 17.167327223634814 chr10 135534747 292790159 2.1602590146126883 19.67788503740406 chr11 135006516 485160155 3.593605474568353 30.490494867573066 chr12 133851895 401955747 3.0029888407631433 23.810752690008705 chr13 115169878 197401225 1.714000469810344 18.00297899638227 chr14 107349540 154272792 1.4371071548140775 14.568472328986676 chr15 102531392 333767553 3.2552718390870963 27.3971479679422 chr16 90354753 216660153 2.397883296742563 19.813541393408773 chr17 81195210 318578547 3.923612575175309 28.533644815557167 chr18 78077248 102881400 1.317687324225362 13.61601842262676 chr19 59128983 330881566 5.5959285820965325 33.48850768865971 chr20 63025520 181525917 2.880197053511022 22.5183296102591 chr21 48129895 43475125 0.9032873435522766 11.845296143553755 chr22 51304566 75830193 1.4780398493186746 13.172873214481202 chrMT 16571 1521390 91.81039164805986 29.45151100078298 chrX 155270560 175689835 1.131507705002159 12.813611303630468 chrY 59373566 1696151 0.028567443633080756 0.9375448769796089