BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506325.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,459,390 number of mapped reads = 4,496,792 (69.62%) number of supplementary alignments = 64,210 (0.99%) number of secondary alignments = 0 number of mapped bases = 349,334,859 bp number of sequenced bases = 349,190,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 669,372 duplication rate = 10.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9378 >>>>>>> ACTG content number of A's = 90,853,228 bp (26.02%) number of C's = 68,458,611 bp (19.6%) number of T's = 100,163,980 bp (28.68%) number of G's = 89,647,076 bp (25.67%) number of N's = 67,586 bp (0.02%) GC percentage = 45.28% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,648,597 number of insertions = 29,412 mapped reads with insertion percentage = 0.64% number of deletions = 68,364 mapped reads with deletion percentage = 1.49% homopolymer indels = 40.44% >>>>>>> Coverage mean coverageData = 0.1128X std coverageData = 0.8312X There is a 6.94% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 26238443 0.10526931846641216 1.310288430650245 chr2 243199373 27967599 0.11499864763220422 0.9861070877606599 chr3 198022430 21737886 0.10977486742284699 0.5018116460612998 chr4 191154276 21252514 0.11117990371295697 0.851169220437481 chr5 180915260 25455553 0.140704288847718 0.5860012789017128 chr6 171115067 12582576 0.07353283507173568 0.4370187760733227 chr7 159138663 17954934 0.11282571853704715 0.8692817283825959 chr8 146364022 21462381 0.14663699935767002 0.9311674176754495 chr9 141213431 9951130 0.07046872191640184 0.794369407785157 chr10 135534747 20564480 0.15172847151882018 1.1950592126695443 chr11 135006516 14840057 0.10992104262582407 0.7945757930545502 chr12 133851895 14949499 0.11168686853480857 0.5272841355752238 chr13 115169878 6796529 0.05901307805501018 0.36961395825755783 chr14 107349540 10104856 0.09413040801106368 0.5385327910699013 chr15 102531392 12937558 0.126181433292157 0.5568571328592892 chr16 90354753 13636438 0.1509210921090117 0.765079926666852 chr17 81195210 9685970 0.11929238190282407 0.6546623860512171 chr18 78077248 6066336 0.07769659094541857 1.1721543423360699 chr19 59128983 9558164 0.1616493894373255 1.058526369312353 chr20 63025520 10076394 0.15987799862658808 0.6960420270102008 chr21 48129895 5624088 0.11685228068750202 0.7387175242441568 chr22 51304566 4530821 0.08831223716033385 0.47665152719031695 chrMT 16571 21247 1.2821797115442641 1.9551504958436225 chrX 155270560 23875110 0.15376456425480786 0.6932142194308918 chrY 59373566 1464296 0.02466242300487729 0.9452139174175974