BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080667.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 = 1,662,219 number of mapped reads = 1,499,214 (90.19%) number of supplementary alignments = 15,415 (0.93%) number of secondary alignments = 0 number of mapped bases = 98,770,987 bp number of sequenced bases = 98,734,162 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,049 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0234 >>>>>>> ACTG content number of A's = 26,481,997 bp (26.82%) number of C's = 18,433,953 bp (18.67%) number of T's = 31,040,183 bp (31.44%) number of G's = 22,773,587 bp (23.07%) number of N's = 4,442 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 681,560 number of insertions = 7,314 mapped reads with insertion percentage = 0.48% number of deletions = 22,830 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.2758X There is a 2.77% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 12046381 0.04833039513269658 0.37264428305260333 chr2 243199373 6549190 0.026929304624481905 0.3963915101953363 chr3 198022430 6153808 0.031076317970646052 0.19658125966813395 chr4 191154276 4173721 0.02183430623335886 0.16767678425728033 chr5 180915260 4481356 0.02477046988739369 0.17501247687525015 chr6 171115067 5881249 0.03437014111679599 0.26732988404438435 chr7 159138663 6212137 0.039036000949687504 0.5629422831058991 chr8 146364022 11694782 0.07990202674261028 0.35607051784731714 chr9 141213431 3133827 0.02219213128530246 0.20453239062538717 chr10 135534747 4705759 0.034719945284584476 0.22919265209690237 chr11 135006516 4082309 0.030237866444905517 0.2095139714226932 chr12 133851895 3184409 0.02379054103044264 0.1730613794893785 chr13 115169878 1979342 0.017186281989462558 0.14694307548526095 chr14 107349540 1950733 0.018171787228897302 0.1559614657833689 chr15 102531392 1750084 0.017068762706352412 0.15515330329024213 chr16 90354753 2619225 0.02898823706595712 0.1953224379523309 chr17 81195210 1582242 0.019486888450685698 0.16294357349043748 chr18 78077248 3144229 0.040270745710709474 0.29456698413551075 chr19 59128983 1765119 0.029852010138581277 0.2477870185648278 chr20 63025520 2580026 0.04093621123633728 0.23163129173593958 chr21 48129895 1444595 0.03001450553756662 0.19731800204826994 chr22 51304566 1006192 0.019612133547723606 0.15494592112726874 chrMT 16571 37075 2.237342345060648 1.781462272944958 chrX 155270560 6396070 0.04119306325680799 0.237313781939435 chrY 59373566 217127 0.003656964110931117 0.07860135774547493