BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085107.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 = 3,705,491 number of mapped reads = 3,104,976 (83.79%) number of supplementary alignments = 18,446 (0.5%) number of secondary alignments = 0 number of mapped bases = 185,988,234 bp number of sequenced bases = 185,928,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,886 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5743 >>>>>>> ACTG content number of A's = 53,269,704 bp (28.65%) number of C's = 38,288,363 bp (20.59%) number of T's = 52,689,290 bp (28.34%) number of G's = 41,677,621 bp (22.42%) number of N's = 4,014 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,576,660 number of insertions = 13,792 mapped reads with insertion percentage = 0.44% number of deletions = 37,216 mapped reads with deletion percentage = 1.19% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0601X std coverageData = 0.4672X There is a 5.01% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 15710158 0.06302956412694354 0.691638031581001 chr2 243199373 17253895 0.07094547484709181 0.5796174233874627 chr3 198022430 11877079 0.05997845294596173 0.30805708181572766 chr4 191154276 11801021 0.06173558471692257 0.3190999765909785 chr5 180915260 9557567 0.052828970867355246 0.26659578206997 chr6 171115067 12994938 0.07594268715098011 0.4632987670468985 chr7 159138663 16832687 0.10577371131991979 0.6159343308415602 chr8 146364022 11871721 0.08111092355742998 0.6407513662878387 chr9 141213431 5624410 0.03982914344741047 0.4337283411278324 chr10 135534747 14440221 0.10654257538843526 0.8412829035243929 chr11 135006516 7761791 0.057491973202241586 0.37574497077168495 chr12 133851895 7084655 0.052929060137699206 0.276431933676505 chr13 115169878 3686194 0.03200658074848356 0.2026230006963347 chr14 107349540 5735972 0.05343266491873184 0.3026773497574121 chr15 102531392 3472624 0.033868885735990006 0.21121869606651875 chr16 90354753 5050914 0.055900922002409766 0.3259237749129349 chr17 81195210 2809836 0.034605933034719656 0.24729117643872633 chr18 78077248 4182964 0.05357468541924019 0.6989190901770628 chr19 59128983 3201674 0.05414728678827437 0.4911095703926843 chr20 63025520 4290600 0.06807718524178777 0.3145856935403944 chr21 48129895 1944367 0.040398322082356504 0.27890311979346216 chr22 51304566 1017723 0.01983688937160096 0.15996022408153643 chrMT 16571 6295 0.37988051415122803 0.7110824497533098 chrX 155270560 7289732 0.046948578017622915 0.299167809505052 chrY 59373566 489196 0.008239289518167058 0.18621866234594717