BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927026.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 = 34,335,180 number of mapped reads = 33,614,167 (97.9%) number of supplementary alignments = 424,616 (1.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,879,900 number of mapped paired reads (second in pair) = 16,734,267 number of mapped paired reads (both in pair) = 33,216,648 number of mapped paired reads (singletons) = 397,519 number of mapped bases = 3,141,062,823 bp number of sequenced bases = 3,138,680,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,819,263 duplication rate = 6.23% >>>>>>> Insert size mean insert size = 131,738.6548 std insert size = 3,578,131.2411 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.2726 >>>>>>> ACTG content number of A's = 904,320,398 bp (28.81%) number of C's = 615,059,005 bp (19.6%) number of T's = 916,874,718 bp (29.21%) number of G's = 702,264,790 bp (22.37%) number of N's = 161,644 bp (0.01%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 29,034,239 number of insertions = 522,682 mapped reads with insertion percentage = 1.53% number of deletions = 1,660,152 mapped reads with deletion percentage = 4.81% homopolymer indels = 53.01% >>>>>>> Coverage mean coverageData = 1.0147X std coverageData = 4.8329X There is a 37.41% of reference with a coverageData >= 1X There is a 22% of reference with a coverageData >= 2X There is a 13.43% of reference with a coverageData >= 3X There is a 8.59% of reference with a coverageData >= 4X There is a 5.63% of reference with a coverageData >= 5X There is a 3.76% of reference with a coverageData >= 6X There is a 2.56% of reference with a coverageData >= 7X There is a 1.76% of reference with a coverageData >= 8X There is a 1.23% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 252619652 1.0135166403457025 7.104615765204837 chr2 243199373 276795537 1.138142477859102 7.9717718084657765 chr3 198022430 215195419 1.0867224435130909 2.1269551709491816 chr4 191154276 194715282 1.0186289633405847 3.13701858826141 chr5 180915260 192117767 1.0619212939803973 1.9929435631910475 chr6 171115067 180790855 1.056545505721013 2.080930691464754 chr7 159138663 163167387 1.0253158090187047 3.2688112135986596 chr8 146364022 160147876 1.0941751518689478 2.4308794812506105 chr9 141213431 132879200 0.9409813150138672 4.947090737519238 chr10 135534747 158382280 1.1685732515515006 11.802236814360418 chr11 135006516 148182781 1.0975972522689201 5.136311745066238 chr12 133851895 139732834 1.043936165416261 2.048310878171429 chr13 115169878 97410966 0.8458024588686288 1.7887993330597767 chr14 107349540 94640625 0.8816118355048378 1.9143997705379998 chr15 102531392 91713961 0.8944963996977628 1.9187801253572332 chr16 90354753 97019037 1.0737568725355267 6.091777699257751 chr17 81195210 78358810 0.9650669048087935 2.4811606232200623 chr18 78077248 83938725 1.0750727920123415 5.185167881965576 chr19 59128983 48991008 0.8285447426011031 4.192950876336818 chr20 63025520 72392982 1.1486296662050548 2.2646019056643176 chr21 48129895 39497660 0.8206471258663665 2.87452870839477 chr22 51304566 36897399 0.719183532319521 1.789382520099369 chrMT 16571 1994269 120.34693138615654 90.20328160846252 chrX 155270560 177966419 1.1461697504021369 2.618622123664818 chrY 59373566 5514092 0.09287116087991076 2.837637299003569