BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104285.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 5,412,594 number of mapped reads = 5,222,337 (96.48%) number of supplementary alignments = 5,452 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,645,421 number of mapped paired reads (second in pair) = 2,576,916 number of mapped paired reads (both in pair) = 5,147,232 number of mapped paired reads (singletons) = 75,105 number of mapped bases = 394,972,250 bp number of sequenced bases = 394,873,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,177,206 duplication rate = 31.85% >>>>>>> Insert size mean insert size = 10,974.3236 std insert size = 981,935.8847 median insert size = 101 >>>>>>> Mapping quality mean mapping quality = 53.9557 >>>>>>> ACTG content number of A's = 103,896,921 bp (26.31%) number of C's = 93,939,324 bp (23.79%) number of T's = 105,891,855 bp (26.82%) number of G's = 90,939,140 bp (23.03%) number of N's = 206,593 bp (0.05%) GC percentage = 46.82% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 2,247,662 number of insertions = 42,030 mapped reads with insertion percentage = 0.8% number of deletions = 46,462 mapped reads with deletion percentage = 0.88% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.1276X std coverageData = 3.1662X There is a 4.85% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% 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 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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% 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 35784659 0.14356898633363888 1.895258979433464 chr2 243199373 29924444 0.12304490604093786 0.9545901760893419 chr3 198022430 24544392 0.12394753463029415 0.9553275786701086 chr4 191154276 20736343 0.10847961883939232 0.8103951080383434 chr5 180915260 21551968 0.11912741910218076 1.0105398744772582 chr6 171115067 23808724 0.13913867678291592 1.0456587059590758 chr7 159138663 19864841 0.1248272457837603 1.006401571262604 chr8 146364022 16482237 0.1126112604366666 1.1091163566111375 chr9 141213431 15200510 0.10764209815141451 0.9412095070084469 chr10 135534747 15786292 0.11647413190655825 0.9989097997796725 chr11 135006516 18156350 0.1344849903392811 1.1442493650494963 chr12 133851895 18024815 0.1346623818811082 1.0978547367954405 chr13 115169878 9810111 0.0851794859068966 0.8706537266504238 chr14 107349540 11863104 0.11050912747273998 1.0339270226177322 chr15 102531392 10664960 0.104016533785087 0.9677345048447066 chr16 90354753 13071482 0.14466844926243116 1.2537201618597706 chr17 81195210 14852481 0.18292311824798532 1.4879382195903252 chr18 78077248 7602686 0.09737389821936347 0.807504596079773 chr19 59128983 15211607 0.25726143471806373 1.9932135047687285 chr20 63025520 7750165 0.1229686799886776 1.047637054802367 chr21 48129895 3948137 0.08203086667859966 0.909409688272151 chr22 51304566 6507981 0.12684993768390906 1.1986192184161721 chrMT 16571 20522861 1238.4805382897835 322.52957117001876 chrX 155270560 12858733 0.08281501013456768 0.6774731608537389 chrY 59373566 442367 0.007450571522013685 0.30548041470916637