Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F2 I1 R1 13 29.1 961540 98.8% 950001 141.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,768,131 A→T pseudogene (911/945 nt) rhsJ → Rhs‑family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,768,1310AT100.0% 89.7 / NA 27pseudogene (911/945 nt)rhsJRhs‑family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (13/14);  total (13/14)

TAATGGTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCAAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTATGATG  >  NC_000913/3767991‑3768269
                                                                                                                                            |                                                                                                                                          
tAATGGTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGc                                                                                                                                    <  2:116610/149‑1 (MQ=255)
     gTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGa                                                                                                                                >  6:22308/1‑148 (MQ=255)
                       cAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGatat                                                                                                                 >  3:70222/1‑145 (MQ=255)
                          tGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAg                                                                                                          >  1:3569/1‑149 (MQ=255)
                          tGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCAAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATAAGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAg                                                                                                          >  6:102110/1‑149 (MQ=255)
                            cTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAgg                                                                                                         <  7:74781/148‑1 (MQ=255)
                            cTAACAGCACCAACGAACATTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGTTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAgg                                                                                                         <  7:73406/148‑1 (MQ=255)
                             tAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGtt                                                                                                       >  2:10105/1‑149 (MQ=255)
                                cAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTa                                                                                                    <  1:10105/149‑1 (MQ=255)
                                  gCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGa                                                                                                  <  8:24454/149‑1 (MQ=255)
                                                           aGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGGTGTAGATGTATGAAAGCATGCTTGTTACTAt                                                                         <  7:7937/149‑1 (MQ=255)
                                                                  aaTGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTa                                                                  >  6:33930/1‑149 (MQ=255)
                                                                             caacaaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTa                                                       >  3:99572/1‑149 (MQ=255)
                                                                                caaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTAttt                                                    >  8:1385/1‑149 (MQ=255)
                                                                                       ccTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAAtt                                             <  7:1385/149‑1 (MQ=255)
                                                                                            gTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATg                                        <  2:116474/149‑1 (MQ=255)
                                                                                                     tAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATATTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGAtg                               >  8:8202/1‑149 (MQ=255)
                                                                                                      aaCATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAACCCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCGTGTTACTAGTTTTTTATGTCTCTTTTATTTGTCAATTGCATGGTGCTGAtgt                              >  3:59038/1‑149 (MQ=255)
                                                                                                              ggCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTAttt                                                    <  4:68935/119‑1 (MQ=255)
                                                                                                              ggCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTAttt                                                    >  3:68935/1‑119 (MQ=255)
                                                                                                              ggCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATaa                      <  5:22308/149‑1 (MQ=255)
                                                                                                                ccATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATaaaa                    <  5:33930/149‑1 (MQ=255)
                                                                                                                    cTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATaaaacaa                 >  7:58063/1‑148 (MQ=255)
                                                                                                                                tttCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATTTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTatga    <  5:102110/149‑1 (MQ=255)
                                                                                                                                   cTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTTAAAATAAAACAAAACGAAAGTatgatg  <  4:99572/148‑1 (MQ=255)
                                                                                                                                      atatGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGaa           >  4:90395/1‑136 (MQ=255)
                                                                                                                                      atatGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGaa           <  3:90395/136‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                          
TAATGGTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCAAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTATGATG  >  NC_000913/3767991‑3768269

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCAAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTATGAT  >  NC_000913/3768013‑3768268
                                                                                                                      |                                                                                                                                         
ACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATA                                                                                                               >  NB501016:228:HFK2FAFXY:2:21110:13029:17768/1‑147 (MQ=60)
   GTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGG                                                                                                        >  NB501016:228:HFK2FAFXY:1:11102:13019:14210/1‑151 (MQ=60)
     GCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGTTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGT                                                                                                       <  NB501016:228:HFK2FAFXY:4:21502:1085:8703/150‑1 (MQ=60)
     GCTAACAGCACCAACGAACATTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGTTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGT                                                                                                       <  NB501016:228:HFK2FAFXY:4:21501:26647:8698/150‑1 (MQ=60)
         ACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAG                                                                                                  <  NB501016:228:HFK2FAFXY:1:11105:16360:16685/151‑1 (MQ=60)
                                    AAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGGTGTAGATGTATGAAAGCATGCTTGTTACTATT                                                                       <  NB501016:228:HFK2FAFXY:4:11406:20374:6547/151‑1 (MQ=60)
                                                      ACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTAT                                                     >  NB501016:228:HFK2FAFXY:2:21306:19332:13850/1‑151 (MQ=60)
                                                                ACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTG                                           <  NB501016:228:HFK2FAFXY:4:11401:16907:17767/151‑1 (MQ=60)
                                                                               TAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAACCCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCGTGTTACTAGTTTTTTATGTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTG                            >  NB501016:228:HFK2FAFXY:2:21102:2926:17420/1‑151 (MQ=60)
                                                                                       GGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAA                    <  NB501016:228:HFK2FAFXY:3:11502:11823:6626/151‑1 (MQ=60)
                                                                                       GGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTG                                                  >  NB501016:228:HFK2FAFXY:2:21109:16514:20191/1‑121 (MQ=60)
                                                                                         GCCATCTTGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAAC                  <  NB501016:228:HFK2FAFXY:3:11508:1888:17015/151‑1 (MQ=60)
                                                                                             TCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGATAATAAATCAAA               >  NB501016:228:HFK2FAFXY:4:21404:25176:5280/1‑150 (MQ=60)
                                                                                                         ATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATTTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTATGAT  <  NB501016:228:HFK2FAFXY:3:21512:25589:15231/151‑1 (MQ=60)
                                                                                                               AATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAA         <  NB501016:228:HFK2FAFXY:2:21212:3490:18309/138‑1 (MQ=60)
                                                                                                                      |                                                                                                                                         
ACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCAAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTATGAT  >  NC_000913/3768013‑3768268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑