BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975259.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,868,670 number of mapped reads = 3,832,412 (99.06%) number of supplementary alignments = 27,041 (0.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,915,964 number of mapped paired reads (second in pair) = 1,916,448 number of mapped paired reads (both in pair) = 3,822,954 number of mapped paired reads (singletons) = 9,458 number of mapped bases = 372,783,133 bp number of sequenced bases = 372,669,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,227 duplication rate = 1.38% >>>>>>> Insert size mean insert size = 111,692.4047 std insert size = 3,178,292.9178 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 53.3826 >>>>>>> ACTG content number of A's = 110,615,832 bp (29.68%) number of C's = 75,676,476 bp (20.31%) number of T's = 109,878,201 bp (29.48%) number of G's = 76,493,329 bp (20.53%) number of N's = 5,394 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,863,603 number of insertions = 52,100 mapped reads with insertion percentage = 1.33% number of deletions = 48,457 mapped reads with deletion percentage = 1.23% homopolymer indels = 37.59% >>>>>>> Coverage mean coverageData = 0.1204X std coverageData = 1.355X There is a 9.48% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 29694769 0.11913618863160225 3.013788399514635 chr2 243199373 32198544 0.13239567027995586 0.9009115605570331 chr3 198022430 25156214 0.1270371947258702 0.43613580274091224 chr4 191154276 26270299 0.1374298265763095 1.0720730921004762 chr5 180915260 22994262 0.1270996266428824 0.4110654257130682 chr6 171115067 21961626 0.12834419776722525 0.7591145072415442 chr7 159138663 20378182 0.1280529923768431 1.045253635917166 chr8 146364022 19198381 0.13116871713186454 2.2777464410419253 chr9 141213431 15687836 0.11109308717242342 1.3371573376467407 chr10 135534747 19069282 0.14069662888735093 2.7348103179477943 chr11 135006516 16611705 0.12304372775607364 0.7113673900443515 chr12 133851895 16358081 0.12221030565163085 0.4007734215593523 chr13 115169878 12455834 0.10815183810475167 0.37435328762594 chr14 107349540 11089099 0.10329898945072331 0.3807731197810015 chr15 102531392 9996774 0.09749964186578097 0.355722585661216 chr16 90354753 10382559 0.11490883052936905 0.7899003464325287 chr17 81195210 9224313 0.11360661546413883 0.608112114093213 chr18 78077248 10450914 0.1338535138943422 1.5919818940409574 chr19 59128983 6320772 0.10689803340605401 1.2772903072842208 chr20 63025520 7081410 0.11235781949914891 0.44394980160630704 chr21 48129895 5150960 0.10702204939362531 0.5081156998496115 chr22 51304566 3755613 0.07320231497524021 0.3133326720981542 chrMT 16571 347345 20.961016233178444 5.797746695920286 chrX 155270560 19931407 0.12836565412013715 0.5238842804995787 chrY 59373566 1016952 0.017128026300458357 0.8154982698183922