BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084280.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 = 2,412,890 number of mapped reads = 2,151,493 (89.17%) number of supplementary alignments = 15,353 (0.64%) number of secondary alignments = 0 number of mapped bases = 141,189,031 bp number of sequenced bases = 141,137,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,741 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8983 >>>>>>> ACTG content number of A's = 39,012,583 bp (27.64%) number of C's = 27,036,425 bp (19.16%) number of T's = 43,177,919 bp (30.59%) number of G's = 31,746,827 bp (22.49%) number of N's = 164,189 bp (0.12%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,464,239 number of insertions = 10,963 mapped reads with insertion percentage = 0.51% number of deletions = 31,676 mapped reads with deletion percentage = 1.46% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.34X There is a 3.97% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 14844748 0.05955751660895561 0.5933632199374052 chr2 243199373 12987389 0.05340223060525736 0.3940741303084505 chr3 198022430 8792449 0.04440127817843666 0.24423574843850387 chr4 191154276 6438478 0.03368210293135164 0.21397312183793174 chr5 180915260 6819076 0.03769209960508583 0.21526409776977595 chr6 171115067 6583928 0.03847661176440997 0.25100961419620843 chr7 159138663 7367840 0.0462982399192332 0.43630067628422997 chr8 146364022 6639234 0.04536110657030182 0.3169397598208769 chr9 141213431 5443114 0.03854529956148434 0.2731109196388328 chr10 135534747 12589747 0.0928894418491813 0.5305170025268727 chr11 135006516 6550407 0.048519191473691534 0.323697220131526 chr12 133851895 7038386 0.052583387033855594 0.25735070125967063 chr13 115169878 3433681 0.02981405433111599 0.19296277616953184 chr14 107349540 4106988 0.03825808662058543 0.22425688837426475 chr15 102531392 3151357 0.03073553317212352 0.19940225317881657 chr16 90354753 3036441 0.03360576947180632 0.22855855353480453 chr17 81195210 4163602 0.05127891165008379 0.26685273319671826 chr18 78077248 3558962 0.04558257483665408 0.47249100880711276 chr19 59128983 3208989 0.05427099938451504 0.4240561702008753 chr20 63025520 2692773 0.042725121506335846 0.23327409000970434 chr21 48129895 1396066 0.029006213290097557 0.1990274595386038 chr22 51304566 1284057 0.02502812322786241 0.17525094281070977 chrMT 16571 120510 7.272343250256472 4.972495814715877 chrX 155270560 8622387 0.05553137053154185 0.2991716019373964 chrY 59373566 318422 0.005363026367659979 0.1133530385758795