BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083643.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 = 1,892,861 number of mapped reads = 1,705,359 (90.09%) number of supplementary alignments = 17,269 (0.91%) number of secondary alignments = 0 number of mapped bases = 112,730,188 bp number of sequenced bases = 112,687,948 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,680 duplication rate = 4.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3515 >>>>>>> ACTG content number of A's = 30,083,129 bp (26.7%) number of C's = 21,124,225 bp (18.75%) number of T's = 35,393,069 bp (31.41%) number of G's = 26,081,822 bp (23.15%) number of N's = 5,703 bp (0.01%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 784,328 number of insertions = 8,464 mapped reads with insertion percentage = 0.49% number of deletions = 26,223 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.75% >>>>>>> Coverage mean coverageData = 0.0364X std coverageData = 0.3237X There is a 3.06% of reference with a coverageData >= 1X There is a 0.44% 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 12330483 0.04947021977529998 0.6222589205106185 chr2 243199373 10330291 0.04247663500349567 0.4779816652315824 chr3 198022430 9287904 0.04690329272295063 0.2531554085304361 chr4 191154276 5014799 0.026234301972925783 0.19494075309142225 chr5 180915260 5222358 0.028866321171580552 0.19574680169415065 chr6 171115067 7511577 0.04389781175727792 0.2959905729522012 chr7 159138663 8116413 0.051002143960452904 0.41275287211032496 chr8 146364022 6012150 0.04107669301407965 0.277071055168764 chr9 141213431 4359053 0.030868543941829443 0.2410365754036777 chr10 135534747 5602039 0.04133286204459437 0.2802853846453994 chr11 135006516 4136999 0.030642958003597398 0.24028925125965334 chr12 133851895 4540740 0.033923613856942404 0.21341875127149862 chr13 115169878 3484240 0.03025304932597046 0.20180672757040513 chr14 107349540 2539102 0.023652658409155737 0.17941546506375197 chr15 102531392 3084481 0.030083284151647918 0.21000444436700763 chr16 90354753 3177310 0.03516483521348346 0.2235183178959884 chr17 81195210 2567357 0.031619562286987125 0.21355511542572972 chr18 78077248 1888353 0.024185701319800617 0.3852996738261545 chr19 59128983 3098048 0.05239474523010145 0.4443971983320485 chr20 63025520 2647528 0.04200723770307647 0.24110069650652538 chr21 48129895 1895051 0.03937367825132384 0.2327574902229436 chr22 51304566 569976 0.011109654450638955 0.11863511106714296 chrMT 16571 2705 0.16323698026673103 0.49188968525190074 chrX 155270560 5091132 0.032788778503793636 0.22005001661908064 chrY 59373566 220099 0.0037070200567033483 0.07916258337352773