BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506013.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 = 6,460,041 number of mapped reads = 4,668,411 (72.27%) number of supplementary alignments = 193 (0%) number of secondary alignments = 0 number of mapped bases = 216,757,376 bp number of sequenced bases = 216,713,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,485 duplication rate = 4.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5035 >>>>>>> ACTG content number of A's = 63,311,712 bp (29.21%) number of C's = 45,248,443 bp (20.88%) number of T's = 62,106,680 bp (28.66%) number of G's = 45,313,581 bp (20.91%) number of N's = 732,769 bp (0.34%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,746,546 number of insertions = 9,390 mapped reads with insertion percentage = 0.2% number of deletions = 31,457 mapped reads with deletion percentage = 0.67% homopolymer indels = 44.11% >>>>>>> Coverage mean coverageData = 0.07X std coverageData = 0.6678X There is a 5.17% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 21521264 0.08634387314124285 1.302340280082392 chr2 243199373 13212257 0.054326854699580165 0.44491774335722023 chr3 198022430 12902735 0.06515794700630631 0.331103470420896 chr4 191154276 9330399 0.048810830682124 0.29568024701495266 chr5 180915260 15255388 0.08432338985666549 0.37868450088800526 chr6 171115067 14870680 0.08690456229666789 0.4393067955619262 chr7 159138663 13903811 0.0873691580530622 0.9269617091812485 chr8 146364022 12620665 0.08622791877091215 0.664483243082228 chr9 141213431 10104971 0.07155814378591226 0.4314999094229066 chr10 135534747 6901834 0.05092298582296391 0.6048133134885421 chr11 135006516 10972900 0.08127681777966925 0.5049993795459244 chr12 133851895 6048473 0.04518780253353903 0.28963659339705605 chr13 115169878 6622540 0.057502361858888136 0.3076634558355862 chr14 107349540 8045268 0.07494459687484455 1.7091286414865825 chr15 102531392 7075112 0.06900434941915155 0.3387820250303425 chr16 90354753 6719727 0.07437048718400016 0.4020156804462259 chr17 81195210 3625181 0.0446477199824965 0.31790742026703833 chr18 78077248 6404728 0.08203065763793314 0.5964689769618864 chr19 59128983 5566531 0.09414217389803575 0.9204037053249505 chr20 63025520 5064255 0.08035245088021487 0.40469886927599447 chr21 48129895 3311209 0.06879734518431839 0.37367909824475004 chr22 51304566 1583966 0.03087378226725473 0.22548175965992304 chrMT 16571 19442 1.173254480719329 1.6582884301167848 chrX 155270560 14372563 0.09256463685066892 0.43705460285230135 chrY 59373566 701477 0.011814634815769698 0.18589538401966135