BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777258.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 = 34,324,464 number of mapped reads = 34,196,805 (99.63%) number of supplementary alignments = 870,745 (2.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,098,417 number of mapped paired reads (second in pair) = 17,098,388 number of mapped paired reads (both in pair) = 34,172,674 number of mapped paired reads (singletons) = 24,131 number of mapped bases = 3,436,519,205 bp number of sequenced bases = 3,436,003,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,863,728 duplication rate = 35.39% >>>>>>> Insert size mean insert size = 157,534.8983 std insert size = 3,929,352.064 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 54.772 >>>>>>> ACTG content number of A's = 943,379,244 bp (27.46%) number of C's = 775,527,304 bp (22.57%) number of T's = 939,936,713 bp (27.36%) number of G's = 777,015,440 bp (22.61%) number of N's = 144,789 bp (0%) GC percentage = 45.18% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 8,711,601 number of insertions = 620,798 mapped reads with insertion percentage = 1.79% number of deletions = 227,087 mapped reads with deletion percentage = 0.65% homopolymer indels = 51.63% >>>>>>> Coverage mean coverageData = 1.1101X std coverageData = 12.7431X There is a 12.5% of reference with a coverageData >= 1X There is a 6.36% of reference with a coverageData >= 2X There is a 4% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 2.55% of reference with a coverageData >= 5X There is a 2.25% of reference with a coverageData >= 6X There is a 2.03% of reference with a coverageData >= 7X There is a 1.87% of reference with a coverageData >= 8X There is a 1.74% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.54% of reference with a coverageData >= 11X There is a 1.47% of reference with a coverageData >= 12X There is a 1.4% of reference with a coverageData >= 13X There is a 1.33% of reference with a coverageData >= 14X There is a 1.28% of reference with a coverageData >= 15X There is a 1.23% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.14% of reference with a coverageData >= 18X There is a 1.1% of reference with a coverageData >= 19X There is a 1.06% of reference with a coverageData >= 20X There is a 1.02% of reference with a coverageData >= 21X There is a 0.99% of reference with a coverageData >= 22X There is a 0.96% of reference with a coverageData >= 23X There is a 0.93% of reference with a coverageData >= 24X There is a 0.9% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.78% of reference with a coverageData >= 30X There is a 0.76% of reference with a coverageData >= 31X There is a 0.74% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.71% of reference with a coverageData >= 34X There is a 0.69% of reference with a coverageData >= 35X There is a 0.67% of reference with a coverageData >= 36X There is a 0.66% of reference with a coverageData >= 37X There is a 0.64% of reference with a coverageData >= 38X There is a 0.63% of reference with a coverageData >= 39X There is a 0.61% of reference with a coverageData >= 40X There is a 0.6% of reference with a coverageData >= 41X There is a 0.59% of reference with a coverageData >= 42X There is a 0.57% of reference with a coverageData >= 43X There is a 0.56% of reference with a coverageData >= 44X There is a 0.55% of reference with a coverageData >= 45X There is a 0.54% of reference with a coverageData >= 46X There is a 0.53% of reference with a coverageData >= 47X There is a 0.51% of reference with a coverageData >= 48X There is a 0.5% of reference with a coverageData >= 49X There is a 0.49% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 347061496 1.3924197845830042 14.070711289421768 chr2 243199373 317510291 1.3055555492735584 13.545532256860854 chr3 198022430 202294609 1.0215742176277707 11.922927502411193 chr4 191154276 150888722 0.789355724378355 10.035699323885677 chr5 180915260 172233316 0.9520109912231837 10.976754776407745 chr6 171115067 163423700 0.955051491754376 11.630261681026266 chr7 159138663 220061802 1.3828305318865222 16.197451883649265 chr8 146364022 113437116 0.7750341542267812 10.829507928659416 chr9 141213431 107881485 0.7639605116598293 8.990123962812504 chr10 135534747 149568535 1.1035438388356604 12.148436758876658 chr11 135006516 227341669 1.6839310852225828 16.831401840192715 chr12 133851895 190159796 1.420673170148245 13.477508934676818 chr13 115169878 100356615 0.8713790163084135 10.863097045292523 chr14 107349540 74469741 0.6937127164215142 9.022106810343983 chr15 102531392 162539722 1.5852678758130974 16.224192409910792 chr16 90354753 107404445 1.1886972343336493 13.11494150310608 chr17 81195210 141138974 1.7382672450751713 15.455361961903236 chr18 78077248 50815501 0.6508362205594131 8.22149789874347 chr19 59128983 185416635 3.135799494471265 25.15298994021714 chr20 63025520 92104352 1.4613818656315727 14.511342623948709 chr21 48129895 23018366 0.4782550637187137 7.229565308219099 chr22 51304566 39535563 0.7706051543248607 8.682352269773917 chrMT 16571 866732 52.30414579687406 26.697193048473736 chrX 155270560 95960526 0.6180213815162385 10.207269521085866 chrY 59373566 1029496 0.01733929877144317 0.5754548149652376