BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084808.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 = 1,705,742 number of mapped reads = 1,532,661 (89.85%) number of supplementary alignments = 19,146 (1.12%) number of secondary alignments = 0 number of mapped bases = 102,438,526 bp number of sequenced bases = 102,400,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,035 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4078 >>>>>>> ACTG content number of A's = 28,111,359 bp (27.45%) number of C's = 19,339,657 bp (18.89%) number of T's = 31,932,136 bp (31.18%) number of G's = 23,002,670 bp (22.46%) number of N's = 14,544 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 781,441 number of insertions = 7,974 mapped reads with insertion percentage = 0.52% number of deletions = 23,410 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.75% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.2484X There is a 2.75% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% 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 9313684 0.037366743411243096 0.32311983340575884 chr2 243199373 9766839 0.040159803372519384 0.3799765411902557 chr3 198022430 9782628 0.04940161576645635 0.2639187408989573 chr4 191154276 5235560 0.02738918589506206 0.19518860558002427 chr5 180915260 5050743 0.027917727890947396 0.19583635374381383 chr6 171115067 4644836 0.027144517905018848 0.20321506819604326 chr7 159138663 5819739 0.036570239376712624 0.25115861421700253 chr8 146364022 5785652 0.03952919522804586 0.2713352911867641 chr9 141213431 6884393 0.04875168708279597 0.2859398665073342 chr10 135534747 3869710 0.028551423790978116 0.2057544707576592 chr11 135006516 4372117 0.03238448876052768 0.2404225763428093 chr12 133851895 4058844 0.030323395869740956 0.20394663042367028 chr13 115169878 2226292 0.01933050584632902 0.16251917545528324 chr14 107349540 1950249 0.018167278592903145 0.15892731915580724 chr15 102531392 2451528 0.023910023575999046 0.18708810607806034 chr16 90354753 1905734 0.021091685126957294 0.17202906444776817 chr17 81195210 3023780 0.03724086679497473 0.23155535722104997 chr18 78077248 4368759 0.05595431591031487 0.33154238969991107 chr19 59128983 1877494 0.03175251635902481 0.24882200972665897 chr20 63025520 1846996 0.02930552576162799 0.20242381964338022 chr21 48129895 540384 0.011227616432572729 0.12643638041485938 chr22 51304566 932081 0.018167603249971943 0.15570739528360308 chrMT 16571 23499 1.4180797779252912 1.5409258462931081 chrX 155270560 6487176 0.04177981969022331 0.2447093718198164 chrY 59373566 219809 0.0037021357282127874 0.0790628833126323