BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083645.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 = 1,948,823 number of mapped reads = 1,609,150 (82.57%) number of supplementary alignments = 11,423 (0.59%) number of secondary alignments = 0 number of mapped bases = 95,911,568 bp number of sequenced bases = 95,881,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,461 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6631 >>>>>>> ACTG content number of A's = 28,402,839 bp (29.62%) number of C's = 18,477,133 bp (19.27%) number of T's = 28,431,588 bp (29.65%) number of G's = 20,557,857 bp (21.44%) number of N's = 12,147 bp (0.01%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 791,364 number of insertions = 6,542 mapped reads with insertion percentage = 0.4% number of deletions = 19,006 mapped reads with deletion percentage = 1.17% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.031X std coverageData = 0.2303X There is a 2.75% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 7690301 0.03085368842471209 0.3331147521445638 chr2 243199373 8291324 0.03409270302682894 0.2304115105797358 chr3 198022430 6583501 0.03324623882254147 0.20015355162408296 chr4 191154276 6603064 0.03454311427488026 0.2067123473849525 chr5 180915260 6135756 0.03391508267461794 0.2024128320101267 chr6 171115067 5445091 0.0318212247200885 0.20642119884248006 chr7 159138663 5360401 0.03368383835171469 0.2883829057023877 chr8 146364022 5086029 0.034749174903105626 0.3054703170693106 chr9 141213431 3963864 0.02807002118658246 0.20364774043113726 chr10 135534747 4569923 0.033717722585190645 0.23368408895936013 chr11 135006516 4338418 0.03213487858615654 0.2080399504323343 chr12 133851895 4261426 0.031836874629231064 0.19688762824149064 chr13 115169878 3262377 0.02832665152254481 0.18476130922292652 chr14 107349540 2900666 0.027020758542607635 0.18574768325190813 chr15 102531392 2797586 0.027285165503263625 0.1821230346127537 chr16 90354753 2420746 0.0267915734327778 0.18652524202908882 chr17 81195210 2230575 0.027471756030928426 0.19055222979041017 chr18 78077248 2573063 0.032955349553303925 0.30042243412231123 chr19 59128983 1602627 0.027103916196224785 0.27976553917937247 chr20 63025520 1845329 0.02927907615835617 0.1920429805790824 chr21 48129895 1236940 0.025700035289917003 0.18082189486628225 chr22 51304566 923340 0.017997228550768758 0.14718989679436645 chrMT 16571 22163 1.3374570031983586 1.3073288375639478 chrX 155270560 5514306 0.035514176029248556 0.21385024389255763 chrY 59373566 252752 0.0042569786022284735 0.09741302279993887