BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708592.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,759,503 number of mapped reads = 5,641,022 (97.94%) number of supplementary alignments = 155 (0%) number of secondary alignments = 0 number of mapped bases = 281,346,030 bp number of sequenced bases = 281,322,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,763 duplication rate = 0.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8093 >>>>>>> ACTG content number of A's = 87,204,222 bp (31%) number of C's = 53,294,003 bp (18.94%) number of T's = 86,785,929 bp (30.85%) number of G's = 54,028,840 bp (19.21%) number of N's = 9,269 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 413,937 number of insertions = 18,036 mapped reads with insertion percentage = 0.32% number of deletions = 14,061 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.0909X std coverageData = 0.3155X There is a 8.32% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.06% 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 21704592 0.08707938986438875 0.31112853550063735 chr2 243199373 24794617 0.1019518130089916 0.3325218703580075 chr3 198022430 20901062 0.10554896230694674 0.3379895038078488 chr4 191154276 21491504 0.11243015039851895 0.34836104382242894 chr5 180915260 18651261 0.10309390705902863 0.3334510760820033 chr6 171115067 19488614 0.11389186435581386 0.3519424200615714 chr7 159138663 15146345 0.09517702809907358 0.32247467761245613 chr8 146364022 15520306 0.10603907837405561 0.3389198734547744 chr9 141213431 11874230 0.08408711491472791 0.3044741608150204 chr10 135534747 11897783 0.0877840056764189 0.3078449483280788 chr11 135006516 13371064 0.0990401381811823 0.33023853010042 chr12 133851895 13585532 0.10149674758060019 0.3326668162654328 chr13 115169878 11393679 0.09892933115723193 0.32984756698552997 chr14 107349540 8567027 0.07980497168408919 0.2967360109435952 chr15 102531392 7404887 0.07222068144749269 0.2823570394079032 chr16 90354753 4984171 0.05516224475761668 0.2455617967838445 chr17 81195210 4888354 0.060204955440105394 0.2565261296475518 chr18 78077248 7672743 0.0982711762586714 0.3256518227998422 chr19 59128983 2429410 0.04108661906124785 0.2092625735928882 chr20 63025520 4185380 0.06640770278452283 0.2683645179224774 chr21 48129895 3459921 0.07188715038750863 0.2837662283019279 chr22 51304566 1654333 0.032245336604153324 0.1873214085468212 chrMT 16571 250 0.01508659706716553 0.12189746369838267 chrX 155270560 15898167 0.10239009249403107 0.33309794161613726 chrY 59373566 380798 0.006413594898443526 0.08464769036439876