BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006179.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 6,686,328 number of mapped reads = 5,984,891 (89.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,997,193 number of mapped paired reads (second in pair) = 2,987,698 number of mapped paired reads (both in pair) = 5,559,528 number of mapped paired reads (singletons) = 425,363 number of mapped bases = 231,862,157 bp number of sequenced bases = 231,833,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,445 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 65,842.8986 std insert size = 2,418,041.9559 median insert size = 132 >>>>>>> Mapping quality mean mapping quality = 48.3374 >>>>>>> ACTG content number of A's = 64,093,528 bp (27.65%) number of C's = 50,280,604 bp (21.69%) number of T's = 65,496,500 bp (28.25%) number of G's = 51,954,234 bp (22.41%) number of N's = 8,318 bp (0%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 660,140 number of insertions = 6,553 mapped reads with insertion percentage = 0.11% number of deletions = 21,813 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0749X std coverageData = 0.4141X There is a 6.21% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 19362672 0.0776835456710858 0.5536228779461995 chr2 243199373 20187376 0.08300751663533278 0.40051209443689484 chr3 198022430 15421144 0.07787574367206786 0.3211340442662971 chr4 191154276 14458614 0.0756384544596847 0.3587866318077456 chr5 180915260 13319927 0.07362522652870741 0.31337129195729085 chr6 171115067 12976846 0.0758369571278022 0.35246201221944023 chr7 159138663 12522052 0.07868642204188935 0.4713491335057211 chr8 146364022 11031078 0.07536741508784174 0.758495423465897 chr9 141213431 9184365 0.06503889137854033 0.33820497742311384 chr10 135534747 11043726 0.0814826178854342 0.4618685133433924 chr11 135006516 11102104 0.08223383825414768 0.38226602321771314 chr12 133851895 9857905 0.07364785534041188 0.31562991734826623 chr13 115169878 6950828 0.06035282940909254 0.2848452040921234 chr14 107349540 7158982 0.06668852050972925 0.34109528474899753 chr15 102531392 7039490 0.0686569241154943 0.30337686174461514 chr16 90354753 7438674 0.08232742332879821 0.39624617653790156 chr17 81195210 6203997 0.07640841128436025 0.329860610893686 chr18 78077248 5934608 0.07600944131637427 0.5509594155423101 chr19 59128983 5452355 0.09221120884152531 0.4777917812726254 chr20 63025520 5106307 0.0810196726659296 0.34093814846610904 chr21 48129895 3102974 0.06447082421434744 0.34434673020688716 chr22 51304566 3323194 0.06477384488546302 0.30773758590182093 chrMT 16571 2058 0.12419286705690664 0.4116764086359167 chrX 155270560 13091459 0.08431385189826068 0.35865278683853885 chrY 59373566 589422 0.00992734712952899 0.2615034088277167