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
A3 F50 I2 R1 193 39.9 1341687 91.8% 1231668 149.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,307,582 C→T C355Y (TGC→TAC)  clsA ← cardiolipin synthase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,307,5820CT97.5% 147.0 / ‑4.5 40C355Y (TGC→TAC) clsAcardiolipin synthase 1
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (21/18);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGCAGTAACCCGCCTTCAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGCAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCAATTGTGTGAATGGTGT  >  NC_000913/1307434‑1307729
                                                                                                                                                    |                                                                                                                                                   
aTGCAGTAACCCGCCTTCAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTaa                                                                                                                                                   <  2:317388/151‑1 (MQ=255)
            gCCTTCAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGt                                                                                                                                       >  2:244375/1‑151 (MQ=255)
              cTTCAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTa                                                                                                                                      >  1:604370/1‑150 (MQ=255)
              cTTCAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTa                                                                                                                                      >  1:390368/1‑150 (MQ=255)
                 cAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTaa                                                                                                                                     <  1:479667/148‑1 (MQ=255)
                    aCTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAatcatc                                                                                                                               <  2:216430/151‑1 (MQ=255)
                          aaaTTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTgg                                                                                                                         >  1:431567/1‑151 (MQ=255)
                          aaaTTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTg                                                                                                                          <  1:582126/150‑1 (MQ=255)
                                  aCCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGt                                                                                                                 >  2:286522/1‑151 (MQ=255)
                                  aCCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGt                                                                                                                 >  2:362836/1‑151 (MQ=255)
                                    cccAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGt                                                                                                                 >  1:200733/1‑149 (MQ=255)
                                      cagcagccagcagTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAggg                                                                                                             >  1:109465/1‑151 (MQ=255)
                                             cagcagTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTc                                                                                                      >  1:103038/1‑151 (MQ=255)
                                              agcagTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTc                                                                                                      >  2:489811/1‑150 (MQ=255)
                                                cagTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATg                                                                                                   >  1:625873/1‑151 (MQ=255)
                                                 agTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGa                                                                                                  <  2:376290/151‑1 (MQ=255)
                                                 agTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCAACGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGGCATGa                                                                                                  <  1:145279/151‑1 (MQ=255)
                                                     ccGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCa                                                                                               <  2:547429/150‑1 (MQ=255)
                                                      cGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCaaa                                                                                             <  2:542824/151‑1 (MQ=255)
                                                         aaaGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAata                                                                                           <  1:515798/150‑1 (MQ=255)
                                                            taatacacgACAGGCCCAGCCGACAAGCATCACGTCATTCTTTCACGGCCCGATAGTACTGACATCCTCCTTTTGTTTCTCAGCCGTGCAAATCGCATGAATTCAATCATCGCTGGGCACTTTTTCGGGCGAGGTCAAGTTCCAATAtt                                                                                         <  1:170683/142‑1 (MQ=255)
                                                              aTGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCAcg                                                                                     <  1:361825/151‑1 (MQ=255)
                                                                     aCTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGa                                                                               >  1:147755/1‑150 (MQ=255)
                                                                        ggCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCGCAAAGTAGGGCGTGGTCATGAGCAAATATTCACGCGCCGAATa                                                                            <  1:603421/150‑1 (MQ=255)
                                                                             aGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGc                                                                      >  1:135560/1‑151 (MQ=255)
                                                                                       cATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCaataat                                                            <  2:348172/151‑1 (MQ=255)
                                                                                         tCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGc                                                          >  2:653571/1‑151 (MQ=255)
                                                                                                           gAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTc                                        >  2:463670/1‑151 (MQ=255)
                                                                                                            aaGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTcc                                       >  1:664903/1‑151 (MQ=255)
                                                                                                              ggATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCgg                                     <  2:317217/151‑1 (MQ=255)
                                                                                                              ggATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCgg                                     <  2:390372/151‑1 (MQ=255)
                                                                                                                  aataCTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGaaa                                  <  2:500194/150‑1 (MQ=255)
                                                                                                                     aCTGACATCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCg                              >  1:610283/1‑151 (MQ=255)
                                                                                                                           aTCCACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGcc                         >  2:564409/1‑150 (MQ=255)
                                                                                                                             ccACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAg                       <  2:43736/150‑1 (MQ=255)
                                                                                                                             ccACCCCGCGCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAg                       <  2:45447/150‑1 (MQ=255)
                                                                                                                                   cgcgCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCa                  <  1:550623/149‑1 (MQ=255)
                                                                                                                                   cgcgCTGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCAAt                >  1:653814/1‑151 (MQ=255)
                                                                                                                                        tGCGCCGCCGTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCAATtgtg            >  2:211581/1‑150 (MQ=255)
                                                                                                                                               ccgTGTAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCAATTGTGTGAATGgt    >  2:113174/1‑151 (MQ=255)
                                                                                                                                                 gtgtAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCAATTGTGTGAATGgtgt  >  1:427156/1‑151 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
ATGCAGTAACCCGCCTTCAAACTGATAAATTTTAACCCCAGCAGCCAGCAGTTCCGTAAAGAATGCGCGACTGGCCCAGCCGACCAGCATCGAGTCATTTTTTCGCGGAAGGATAATACTGACATCCACCCCGCGCTGCGCCGCCGTGCAAATCGCATGAAGTAAATCATCGCTTGGCACAAAGTAGGGCGTGGTCATGATCAAATATTCACGCGCCGAATAAGCCGCAGTCAATAATGCCTGGTGAATGAGATCTTCCGGAAAGCCGGGGCCAGAAGCAATTGTGTGAATGGTGT  >  NC_000913/1307434‑1307729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A