BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124846.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 88,870,426 number of mapped reads = 84,415,516 (94.99%) number of supplementary alignments = 2,732,501 (3.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 43,454,945 number of mapped paired reads (second in pair) = 40,960,571 number of mapped paired reads (both in pair) = 81,503,164 number of mapped paired reads (singletons) = 2,912,352 number of mapped bases = 10,905,635,877 bp number of sequenced bases = 10,895,163,613 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,420,523 duplication rate = 21.42% >>>>>>> Insert size mean insert size = 191,553.9003 std insert size = 4,153,181.6226 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 52.8287 >>>>>>> ACTG content number of A's = 3,129,666,812 bp (28.73%) number of C's = 2,108,387,155 bp (19.35%) number of T's = 3,235,827,207 bp (29.7%) number of G's = 2,421,098,407 bp (22.22%) number of N's = 184,032 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 149,705,195 number of insertions = 2,698,144 mapped reads with insertion percentage = 2.89% number of deletions = 4,257,972 mapped reads with deletion percentage = 4.76% homopolymer indels = 42.03% >>>>>>> Coverage mean coverageData = 3.5228X std coverageData = 65.9093X There is a 54.91% of reference with a coverageData >= 1X There is a 42.31% of reference with a coverageData >= 2X There is a 33.18% of reference with a coverageData >= 3X There is a 26.82% of reference with a coverageData >= 4X There is a 21.94% of reference with a coverageData >= 5X There is a 18.19% of reference with a coverageData >= 6X There is a 15.23% of reference with a coverageData >= 7X There is a 12.85% of reference with a coverageData >= 8X There is a 10.93% of reference with a coverageData >= 9X There is a 9.35% of reference with a coverageData >= 10X There is a 8.05% of reference with a coverageData >= 11X There is a 6.97% of reference with a coverageData >= 12X There is a 6.06% of reference with a coverageData >= 13X There is a 5.29% of reference with a coverageData >= 14X There is a 4.64% of reference with a coverageData >= 15X There is a 4.08% of reference with a coverageData >= 16X There is a 3.6% of reference with a coverageData >= 17X There is a 3.19% of reference with a coverageData >= 18X There is a 2.84% of reference with a coverageData >= 19X There is a 2.53% of reference with a coverageData >= 20X There is a 2.26% of reference with a coverageData >= 21X There is a 2.02% of reference with a coverageData >= 22X There is a 1.82% of reference with a coverageData >= 23X There is a 1.63% of reference with a coverageData >= 24X There is a 1.47% of reference with a coverageData >= 25X There is a 1.33% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.1% of reference with a coverageData >= 28X There is a 1% of reference with a coverageData >= 29X There is a 0.91% of reference with a coverageData >= 30X There is a 0.83% of reference with a coverageData >= 31X There is a 0.76% of reference with a coverageData >= 32X There is a 0.7% of reference with a coverageData >= 33X There is a 0.64% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.55% of reference with a coverageData >= 36X There is a 0.5% of reference with a coverageData >= 37X There is a 0.47% of reference with a coverageData >= 38X There is a 0.43% of reference with a coverageData >= 39X There is a 0.4% of reference with a coverageData >= 40X There is a 0.37% of reference with a coverageData >= 41X There is a 0.35% of reference with a coverageData >= 42X There is a 0.32% of reference with a coverageData >= 43X There is a 0.3% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 885257723 3.551677100936892 28.859897681026457 chr2 243199373 942114485 3.8738359946347396 79.65215164981359 chr3 198022430 741124136 3.7426272165228958 8.715218276209844 chr4 191154276 709189977 3.7100398266790537 87.75293119795441 chr5 180915260 630404464 3.484528966765988 9.583639416138288 chr6 171115067 615293065 3.5957854313320055 15.840889792637245 chr7 159138663 623690098 3.919161354271275 26.942493079564464 chr8 146364022 628694254 4.295415262638793 12.786191160119177 chr9 141213431 434858400 3.0794407934185806 61.975955067527906 chr10 135534747 675309180 4.9825538833964105 220.29921881840403 chr11 135006516 427663063 3.1677216453759907 15.396614785750147 chr12 133851895 471928174 3.5257489182353376 21.03067170445215 chr13 115169878 290997924 2.526684312368552 5.537632261398083 chr14 107349540 350366449 3.263790874185395 9.996734667275687 chr15 102531392 283412803 2.764156396121102 10.388751832217924 chr16 90354753 415264590 4.595935202213435 99.41918320545382 chr17 81195210 244957497 3.01689591048536 43.531243138594654 chr18 78077248 244752054 3.1347423259590297 54.95000883679992 chr19 59128983 150409386 2.5437506002766868 16.921109769617825 chr20 63025520 226961056 3.6010977140688407 29.306704616831926 chr21 48129895 130943562 2.720628457635322 43.3732809850262 chr22 51304566 97491052 1.9002412377876854 9.77795790581298 chrMT 16571 3484933 210.3031199082735 113.7530857759452 chrX 155270560 399790651 2.5748000844461436 10.596180160099344 chrY 59373566 281276901 4.737409590658577 148.2954577782038