BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695944.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 422,994,434 number of mapped reads = 419,450,885 (99.16%) number of supplementary alignments = 5,529,242 (1.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 210,439,309 number of mapped paired reads (second in pair) = 209,011,576 number of mapped paired reads (both in pair) = 417,133,452 number of mapped paired reads (singletons) = 2,317,433 number of mapped bases = 41,574,079,629 bp number of sequenced bases = 41,562,963,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,750,637 duplication rate = 18.48% >>>>>>> Insert size mean insert size = 72,842.3658 std insert size = 2,650,946.6909 median insert size = 315 >>>>>>> Mapping quality mean mapping quality = 54.0379 >>>>>>> ACTG content number of A's = 11,723,172,682 bp (28.21%) number of C's = 8,968,537,852 bp (21.58%) number of T's = 11,638,012,136 bp (28%) number of G's = 9,232,075,510 bp (22.21%) number of N's = 1,165,175 bp (0%) GC percentage = 43.79% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 183,809,845 number of insertions = 5,339,587 mapped reads with insertion percentage = 1.24% number of deletions = 4,528,716 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 13.4296X std coverageData = 32.2252X There is a 82.26% of reference with a coverageData >= 1X There is a 74.96% of reference with a coverageData >= 2X There is a 68.61% of reference with a coverageData >= 3X There is a 62.97% of reference with a coverageData >= 4X There is a 57.92% of reference with a coverageData >= 5X There is a 53.38% of reference with a coverageData >= 6X There is a 49.3% of reference with a coverageData >= 7X There is a 45.61% of reference with a coverageData >= 8X There is a 42.28% of reference with a coverageData >= 9X There is a 39.26% of reference with a coverageData >= 10X There is a 36.51% of reference with a coverageData >= 11X There is a 34.02% of reference with a coverageData >= 12X There is a 31.74% of reference with a coverageData >= 13X There is a 29.66% of reference with a coverageData >= 14X There is a 27.76% of reference with a coverageData >= 15X There is a 26.01% of reference with a coverageData >= 16X There is a 24.41% of reference with a coverageData >= 17X There is a 22.94% of reference with a coverageData >= 18X There is a 21.58% of reference with a coverageData >= 19X There is a 20.32% of reference with a coverageData >= 20X There is a 19.17% of reference with a coverageData >= 21X There is a 18.09% of reference with a coverageData >= 22X There is a 17.1% of reference with a coverageData >= 23X There is a 16.17% of reference with a coverageData >= 24X There is a 15.31% of reference with a coverageData >= 25X There is a 14.51% of reference with a coverageData >= 26X There is a 13.77% of reference with a coverageData >= 27X There is a 13.07% of reference with a coverageData >= 28X There is a 12.42% of reference with a coverageData >= 29X There is a 11.81% of reference with a coverageData >= 30X There is a 11.24% of reference with a coverageData >= 31X There is a 10.71% of reference with a coverageData >= 32X There is a 10.2% of reference with a coverageData >= 33X There is a 9.73% of reference with a coverageData >= 34X There is a 9.29% of reference with a coverageData >= 35X There is a 8.87% of reference with a coverageData >= 36X There is a 8.48% of reference with a coverageData >= 37X There is a 8.11% of reference with a coverageData >= 38X There is a 7.76% of reference with a coverageData >= 39X There is a 7.43% of reference with a coverageData >= 40X There is a 7.11% of reference with a coverageData >= 41X There is a 6.82% of reference with a coverageData >= 42X There is a 6.54% of reference with a coverageData >= 43X There is a 6.27% of reference with a coverageData >= 44X There is a 6.02% of reference with a coverageData >= 45X There is a 5.79% of reference with a coverageData >= 46X There is a 5.56% of reference with a coverageData >= 47X There is a 5.35% of reference with a coverageData >= 48X There is a 5.14% of reference with a coverageData >= 49X There is a 4.95% of reference with a coverageData >= 50X There is a 4.76% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5248067421 21.055383533026383 45.88980769884769 chr2 243199373 3226356407 13.266302323073834 43.92732260512977 chr3 198022430 2636905966 13.316198402372903 19.998731973934987 chr4 191154276 2150403226 11.249569044429851 20.351803276748218 chr5 180915260 2334604976 12.904411579211173 19.837446225012034 chr6 171115067 1536714600 8.980591989599606 19.84638302349818 chr7 159138663 2999213121 18.84653964322925 28.457758703231683 chr8 146364022 1430280611 9.772077806115494 18.817141701997155 chr9 141213431 1290734266 9.140308091515742 38.92956424655362 chr10 135534747 2083028422 15.368962337016058 44.03325990729955 chr11 135006516 2425187206 17.96348263664548 29.54095555905401 chr12 133851895 2019665462 15.088807386701548 25.2304024535765 chr13 115169878 804120896 6.98204174532511 16.973916800428974 chr14 107349540 1355416175 12.626194532365952 26.79433626887018 chr15 102531392 924608090 9.017804907983693 17.710981674120926 chr16 90354753 1455744854 16.11143637346892 40.96283912341197 chr17 81195210 1568678391 19.319839076714008 37.559549253372474 chr18 78077248 1331571090 17.054534119850125 48.45523557045159 chr19 59128983 1335534086 22.586792774704072 43.2392508089264 chr20 63025520 1124255834 17.83810485022575 29.120459703843473 chr21 48129895 509178201 10.579250193668614 24.486842936122162 chr22 51304566 985751213 19.21371312253182 43.3013361630704 chrMT 16571 6580273 397.0957093717941 137.4307938839446 chrX 155270560 618458504 3.9831021669529627 12.228433217515114 chrY 59373566 173020338 2.91409712530994 37.712848396514424