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
A1 F28 I1 R1	112	94.0	3211786	99.3%	3189303	138.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,143,408	T→C	T253A (ACC→GCC)	hybB ←	hydrogenase 2 membrane subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,143,408	0	T	C	97.7%	145.6 / ‑5.8	44	T253A (ACC→GCC)	hybB	hydrogenase 2 membrane subunit
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (22/21); total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GCGGGAAGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGTGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAACGCCGTCAGCAGCGAGAACAGCGGCAA  >  NC_000913/3143270‑3143540

gCGGGAAGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCT‑‑CCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGtt                                                                                                                                   >  2:1014723/1‑140 (MQ=255)

  gggAAGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGtt                                                                                                                                   >  1:178916/1‑140 (MQ=255)

    gAAGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTgg                                                                                                                                 <  1:1594551/140‑1 (MQ=255)

     aaGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGt                                                                                                                                <  2:906673/140‑1 (MQ=255)

     aaGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGt                                                                                                                                <  2:2432/140‑1 (MQ=255)

     aaGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGt                                                                                                                                <  1:1502799/140‑1 (MQ=255)

     aaGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCT‑‑CCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCa                                                                                                                              <  1:1014723/140‑1 (MQ=255)

       gagCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCa                                                                                                                              <  1:750185/140‑1 (MQ=255)

       gagCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCa                                                                                                                              <  1:1225731/140‑1 (MQ=255)

                 agGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTaacaaa                                                                                                                    <  1:689102/140‑1 (MQ=255)

                  ggACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTa                                                                                                                         <  2:867409/134‑1 (MQ=255)

                  ggACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTa                                                                                                                         >  1:867409/1‑134 (MQ=255)

                   gACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTaacaaaca                                                                                                                  >  2:608646/1‑140 (MQ=255)

                   gACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTaacaaaca                                                                                                                  <  2:1463785/140‑1 (MQ=255)

                     cTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGa                                                                                                                <  2:662735/140‑1 (MQ=255)

                     cTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGa                                                                                                                <  1:1246095/140‑1 (MQ=255)

                     cTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGa                                                                                                                <  1:1163608/140‑1 (MQ=255)

                     cTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGa                                                                                                                <  1:318774/140‑1 (MQ=255)

                        cAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGActc                                                                                                             >  2:1006685/1‑140 (MQ=255)

                          aTCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCtt                                                                                                           <  1:1006685/140‑1 (MQ=255)

                                aaCATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATc                                                                                                     <  2:537376/140‑1 (MQ=255)

                                aaCATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATc                                                                                                     <  1:608646/140‑1 (MQ=255)

                                  cATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAACACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCg                                                                                                   <  2:998530/140‑1 (MQ=255)

                                     cACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGAc                                                                                                <  1:823735/140‑1 (MQ=255)

                                     cACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGAc                                                                                                <  1:113774/140‑1 (MQ=255)

                                                    aCCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGAc                                                                                 >  1:565711/1‑140 (MQ=255)

                                                      cGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGAccc                                                                               >  1:1190156/1‑140 (MQ=255)

                                                      cGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTACCACGCAGAccc                                                                               >  1:109178/1‑140 (MQ=255)

                                                        gCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCTAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGc                                                                             >  2:841374/1‑140 (MQ=255)

                                                                        gCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAATCAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCt                                                             >  1:678111/1‑140 (MQ=255)

                                                                         cTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCAGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCtt                                                            >  1:237062/1‑140 (MQ=255)

                                                                             tCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCaaa                                                        >  1:1510487/1‑140 (MQ=255)

                                                                              cgcgATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAg                                                       >  1:291380/1‑140 (MQ=255)

                                                                                         accTCGCAAAAGCGCAGCACGAAAAAAACCGCCAGCAACACACTGAGGGGTTTGGTCAGCTAAACAAACAGCCTCTTTCCATCCGGACCGTTCCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCga                                            <  2:1434578/138‑1 (MQ=255)

                                                                                         aGCTCCCTAAGGCGCAGCACGAAAAAAACCGCCACCAACACACGAATGGCGTGGGTTAGTTTAAAAAACAGCCTCTTTTCATCAGGACCTTGCCCACGCAGTCCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCga                                            <  2:843300/140‑1 (MQ=255)

                                                                                           cTCGCAAAAGCGCAGCACGAAAAAAACCGCCAGCAACACACTGATGGGGTTGGTCAGCTTAAAAAACAGACTCTTTCCATCCGGCCCGTTGCCACGCAGCCCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCgaga                                          <  2:625266/140‑1 (MQ=255)

                                                                                              gCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGc                                       >  1:1523532/1‑140 (MQ=255)

                                                                                               ccAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGcc                                      >  1:1434578/1‑140 (MQ=255)

                                                                                               ccAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGcc                                      >  1:247573/1‑140 (MQ=255)

                                                                                               ccAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGcc                                      >  1:990082/1‑140 (MQ=255)

                                                                                               ccAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGcc                                      >  1:434028/1‑140 (MQ=255)

                                                                                                cAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGccc                                     >  1:242189/1‑140 (MQ=255)

                                                                                                cAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCCAACCTTCAAAGATGACAAACGAGAAGccc                                     >  2:1180397/1‑140 (MQ=255)

                                                                                                        agcaCGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGaa                             >  1:562065/1‑140 (MQ=255)

                                                                                                        agcaCGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACACGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGaa                             >  2:468109/1‑140 (MQ=255)

                                                                                                         gcaCGATGAAAATCGCCAGCAACACACTGATGGCGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAAc                            <  1:138624/140‑1 (MQ=255)

                                                                                                               tGAAAATCGCCAGCAACACACTGATGGTGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAACGCCGTc                      >  2:1384803/1‑140 (MQ=255)

                                                                                                                           gCAACACACTGAGGGGGTTGTTCAGCTTAACAAACACACTCTTTTCTTCCGAACGGTTGCCAGGCGGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAACGCCGTCAGCAGCGAGAAc          <  2:1488426/140‑1 (MQ=255)

                                                                                                                                ccacTGATGGCGTGGGTCAGCTTAACAAACAGCCTCTTTTCATCCGGACCGTTGCCACGCAGCCCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAACGCCGTCAGCAGCGAGAACAGCgg     <  2:562065/139‑1 (MQ=255)

                                                                                                                                   cTGATGGGGTTGGTCAGCTAAAAAAACAGACTTTTTTCACCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAACGCCGTCAGCAGCGAGAACAGCGGCaa  <  2:434028/140‑1 (MQ=255)

GCGGGAAGAGCATCAGCAGGACTTCAATCCAGAACATCACGGAGTAGAAGTCACCGGCAAACGCTAACGACAGCTTGTCGCGATAGATAAGCTCGCCAAAGCGCAGCACGATGAAAATCGCCAGCAACACACTGATGGTGTTGGTCAGCTTAACAAACAGACTCTTTTCATCCGGACCGTTGCCACGCAGACCCGCCTGCACCAGCGAACCTTCAAAGATGACAATCGAGAAGCCCATGATGAACGCCGTCAGCAGCGAGAACAGCGGCAA  >  NC_000913/3143270‑3143540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A