BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081783.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,012,558 number of mapped reads = 2,751,743 (91.34%) number of supplementary alignments = 17,711 (0.59%) number of secondary alignments = 0 number of mapped bases = 185,812,283 bp number of sequenced bases = 185,736,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,924 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0782 >>>>>>> ACTG content number of A's = 51,128,506 bp (27.53%) number of C's = 35,957,168 bp (19.36%) number of T's = 56,545,705 bp (30.44%) number of G's = 42,102,771 bp (22.67%) number of N's = 2,003 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,590,514 number of insertions = 14,248 mapped reads with insertion percentage = 0.51% number of deletions = 42,524 mapped reads with deletion percentage = 1.53% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.5664X There is a 5.05% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% 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 14763257 0.05923057258902476 1.029515638698798 chr2 243199373 15875050 0.06527586730250329 0.7414777353939328 chr3 198022430 12332002 0.06227578360693786 0.28951870799073925 chr4 191154276 12262474 0.06414961912753654 0.35882443293972666 chr5 180915260 11334056 0.06264842446126435 0.2887482866220735 chr6 171115067 10761431 0.06289002592623828 0.36472532818756676 chr7 159138663 10290135 0.06466143931346212 0.8323262509073757 chr8 146364022 9405934 0.06426397602000852 0.6231741179343491 chr9 141213431 7783493 0.05511864519459201 0.5311684297864319 chr10 135534747 8924267 0.06584486412181816 0.6735065578073739 chr11 135006516 8386388 0.06211839434475889 0.46964492508422917 chr12 133851895 8357781 0.062440513076038255 0.2924487912528828 chr13 115169878 5862810 0.05090575853523089 0.2566340783647522 chr14 107349540 5617413 0.05232824472279993 0.3082062597059536 chr15 102531392 5233369 0.051041626353809766 0.26319109158837384 chr16 90354753 5305622 0.05871989932837291 0.3597609359897454 chr17 81195210 4993836 0.06150407148401981 0.3285551344761804 chr18 78077248 4998517 0.06402014835358952 1.0357500187492827 chr19 59128983 3886648 0.06573169032858218 0.8006411004121835 chr20 63025520 3692192 0.05858249166369433 0.30061317562089646 chr21 48129895 2386577 0.04958616676807626 0.3050517313805274 chr22 51304566 2032218 0.039610860366697184 0.2264233905681083 chrMT 16571 20610 1.2437390622171263 1.3694140959340582 chrX 155270560 10761504 0.0693080774616901 0.3828045916797789 chrY 59373566 544699 0.00917409946372431 0.2527095311556995