BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549008.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,226,955 number of mapped reads = 9,766,445 (86.99%) number of secondary alignments = 0 number of mapped bases = 387,478,828 bp number of sequenced bases = 387,436,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 928,832 duplication rate = 8.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4342 >>>>>>> ACTG content number of A's = 115,109,111 bp (29.71%) number of C's = 77,456,307 bp (19.99%) number of T's = 116,054,297 bp (29.95%) number of G's = 78,812,837 bp (20.34%) number of N's = 3,862 bp (0%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,146,546 number of insertions = 12,088 mapped reads with insertion percentage = 0.12% number of deletions = 32,745 mapped reads with deletion percentage = 0.34% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 0.1252X std coverageData = 0.8685X There is a 9.22% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 31082862 0.12470525399413147 1.3994055156422516 chr2 243199373 33943478 0.13957058186988006 0.7207395909403651 chr3 198022430 27466615 0.1387045649323665 0.47530148296702623 chr4 191154276 27278478 0.1427039905714691 0.5446174140219161 chr5 180915260 25077516 0.1386147083446692 0.48413925721689005 chr6 171115067 23550967 0.13763233952975046 0.5700808829273537 chr7 159138663 21621451 0.1358654810364971 1.0447858036718842 chr8 146364022 20601600 0.14075590243072167 2.14413216037357 chr9 141213431 16491268 0.11678257431476188 0.6875139710455256 chr10 135534747 18336750 0.13529187463639858 0.7873728452949249 chr11 135006516 17847619 0.1321982044185186 0.6425250038669887 chr12 133851895 17986615 0.13437699182368693 0.48963592592038263 chr13 115169878 13185933 0.11449116061406264 0.4263461591825651 chr14 107349540 12153125 0.11321077854641948 0.5290448839237771 chr15 102531392 10911347 0.10641957343171543 0.41045455713926005 chr16 90354753 10201553 0.11290554908605638 0.4928402489573776 chr17 81195210 9365938 0.11535086860419476 0.48763000498741915 chr18 78077248 10772301 0.13796978346367947 1.419648590236174 chr19 59128983 6394797 0.1081499575259057 1.1215564925516164 chr20 63025520 7841299 0.12441466567828396 0.4839200614276489 chr21 48129895 5044075 0.10480128826377036 0.5406345691628925 chr22 51304566 3760462 0.07329682898009507 0.36899323384592103 chrMT 16571 9479 0.5720234143986482 0.9750613712711473 chrX 155270560 13211804 0.08508891833712715 0.5051215265954544 chrY 59373566 3341496 0.056279186599639305 0.5501150935560458