BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818931.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 696,651 number of mapped reads = 661,484 (94.95%) number of supplementary alignments = 9,063 (1.3%) number of secondary alignments = 0 number of mapped bases = 61,293,064 bp number of sequenced bases = 61,259,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,444 duplication rate = 22.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0847 >>>>>>> ACTG content number of A's = 17,867,244 bp (29.17%) number of C's = 13,161,774 bp (21.49%) number of T's = 17,744,813 bp (28.97%) number of G's = 12,483,308 bp (20.38%) number of N's = 2,821 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 389,665 number of insertions = 7,831 mapped reads with insertion percentage = 1.15% number of deletions = 18,129 mapped reads with deletion percentage = 2.68% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.2611X There is a 1.37% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 7182513 0.02881642970911595 0.44036207970276053 chr2 243199373 5425950 0.022310707190844607 0.3531580973817352 chr3 198022430 4059651 0.020500965471436747 0.19499649537968178 chr4 191154276 3945963 0.020642818369388714 0.20709322406926273 chr5 180915260 3166767 0.01750414531090412 0.18251874533064225 chr6 171115067 3364431 0.019661804532969618 0.20006893276114543 chr7 159138663 3102587 0.019496123327365143 0.23143229167763288 chr8 146364022 4018066 0.02745255251321257 0.2532742912980962 chr9 141213431 2277223 0.016126107721297418 0.2901525534569327 chr10 135534747 3064837 0.022612924492344387 0.3152728236925516 chr11 135006516 2316404 0.017157720002196043 0.19649458196658154 chr12 133851895 2747752 0.02052830107485591 0.1980456564021667 chr13 115169878 1010603 0.008774889906543099 0.12553991387338895 chr14 107349540 1540383 0.01434922776567091 0.17417064850185993 chr15 102531392 1790120 0.017459238239933384 0.178905665641933 chr16 90354753 1845844 0.02042885336646319 0.26862356512842206 chr17 81195210 1324375 0.01631099913406222 0.18741274373759315 chr18 78077248 1559441 0.0199730528412067 0.3438069241120335 chr19 59128983 917950 0.01552453557335833 0.34563135804407474 chr20 63025520 1190207 0.0188845248718297 0.1959388929881761 chr21 48129895 832042 0.017287426037393184 0.19159965785160143 chr22 51304566 727690 0.014183727818689667 0.1686552412746087 chrMT 16571 23996 1.4480719328948162 1.849564461753811 chrX 155270560 3676389 0.02367730882145334 0.2377405867961112 chrY 59373566 181880 0.0030633160891835264 0.15904385970822063