BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082665.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 = 3,322,851 number of mapped reads = 2,970,033 (89.38%) number of supplementary alignments = 13,652 (0.41%) number of secondary alignments = 0 number of mapped bases = 197,531,919 bp number of sequenced bases = 197,455,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,282 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9801 >>>>>>> ACTG content number of A's = 54,186,802 bp (27.44%) number of C's = 34,433,837 bp (17.44%) number of T's = 65,028,273 bp (32.93%) number of G's = 43,753,023 bp (22.16%) number of N's = 53,581 bp (0.03%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,870,168 number of insertions = 18,221 mapped reads with insertion percentage = 0.61% number of deletions = 47,309 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.0638X std coverageData = 0.5064X There is a 5.27% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 19355659 0.0776554093319591 0.6813276292205674 chr2 243199373 21031729 0.08647937180331464 0.7666796772050933 chr3 198022430 13765758 0.06951615531634472 0.3063232350533262 chr4 191154276 11586087 0.06061118402603769 0.29943049835221164 chr5 180915260 10949679 0.060523799927103994 0.2872938008786707 chr6 171115067 12993541 0.0759345230540102 0.5674491021042146 chr7 159138663 10410759 0.06541941979241085 0.546556980870951 chr8 146364022 15492414 0.10584851241652815 0.6053188625126549 chr9 141213431 5761309 0.040798590893241594 0.5520209634062604 chr10 135534747 7518548 0.05547321381726562 0.4028959583019788 chr11 135006516 8249735 0.061106198755621545 0.4637047778656436 chr12 133851895 6198736 0.04631040897852062 0.2638435947951888 chr13 115169878 4386126 0.03808396844876401 0.2218290404916873 chr14 107349540 4383764 0.04083635570306123 0.3220560192947008 chr15 102531392 4047917 0.03947978195790027 0.2280989059362635 chr16 90354753 7826316 0.08661764589185474 0.3906903154757814 chr17 81195210 4952269 0.060992132417663554 0.3741870062590769 chr18 78077248 6855161 0.0877997262403511 1.2413544111193737 chr19 59128983 2567217 0.04341723584185441 0.5739804910864089 chr20 63025520 3817200 0.060565942177073666 0.32981268186937857 chr21 48129895 4481914 0.09312120876224642 0.3733093885206222 chr22 51304566 2571337 0.050119067375016875 0.2595398011854218 chrMT 16571 6205 0.3744493392070485 0.6723632501605633 chrX 155270560 7988340 0.0514478726681993 0.3458575401604536 chrY 59373566 334199 0.0056287506800585295 0.12444915288105522