BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472829.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 3,076,015 number of mapped reads = 2,590,740 (84.22%) number of supplementary alignments = 25,292 (0.82%) number of secondary alignments = 0 number of mapped bases = 168,164,197 bp number of sequenced bases = 168,096,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,394 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9112 >>>>>>> ACTG content number of A's = 45,210,630 bp (26.9%) number of C's = 33,601,476 bp (19.99%) number of T's = 49,842,453 bp (29.65%) number of G's = 39,437,920 bp (23.46%) number of N's = 3,889 bp (0%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,429,063 number of insertions = 13,506 mapped reads with insertion percentage = 0.52% number of deletions = 37,507 mapped reads with deletion percentage = 1.43% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.3913X There is a 4.69% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 12431256 0.04987452368273137 0.4880323600386302 chr2 243199373 16173999 0.06650510155714916 0.5973517710236552 chr3 198022430 11900098 0.06009469735322408 0.27345771481841247 chr4 191154276 9059460 0.04739344674664772 0.2833699146294191 chr5 180915260 8352212 0.046166431731629494 0.2421926471108184 chr6 171115067 10453199 0.0610887117263613 0.3067883977198159 chr7 159138663 10363267 0.06512098822898871 0.506761242255829 chr8 146364022 9441372 0.06450609836343524 0.3821439454091102 chr9 141213431 9702704 0.06870949831960389 0.4683381854855547 chr10 135534747 6996354 0.05162037156420117 0.3622958006508673 chr11 135006516 6326235 0.04685873828489878 0.38711381237927117 chr12 133851895 6830035 0.051026808398939735 0.2638177835376852 chr13 115169878 6793369 0.05898564032515516 0.28200589942918414 chr14 107349540 3219505 0.02999085976521185 0.24799402238320634 chr15 102531392 2993472 0.02919566331450957 0.2185918002401399 chr16 90354753 5658970 0.06263057351282893 0.32240516569547345 chr17 81195210 3754101 0.04623549837484255 0.2697206751126222 chr18 78077248 2785734 0.03567920324240936 0.7912760018325466 chr19 59128983 3992124 0.06751551941963893 0.4154228292491155 chr20 63025520 7407619 0.11753364351456362 0.41432544472470156 chr21 48129895 2436384 0.05062101215886716 0.30610576466237716 chr22 51304566 2005059 0.03908149227887436 0.2387220145889478 chrMT 16571 19870 1.1990827348983164 1.1841749766249168 chrX 155270560 8176038 0.05265671740991982 0.3003156415673667 chrY 59373566 891761 0.015019495376107273 0.203200228550198