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
A11 F28 I1 R1	134	60.5	2175152	94.0%	2044642	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,216,781	G→A	M1M (ATG→ATA) †	nfeR →	DNA‑binding transcriptional repressor NfeR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,216,781	0	G	A	98.0%	166.3 / ‑5.6	49	M1M (ATG→ATA) †	nfeR	DNA‑binding transcriptional repressor NfeR
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (21/27); total (21/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCG  >  NC_000913/3216644‑3216908

cGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAg                                                                                                                               >  2:470565/1‑140 (MQ=255)

     gATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCcatc                                                                                                                          >  2:977035/1‑140 (MQ=255)

     gATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCcatc                                                                                                                          <  2:477971/140‑1 (MQ=255)

     gATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCcatc                                                                                                                          <  2:440418/140‑1 (MQ=255)

     gATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCcatc                                                                                                                          >  1:440418/1‑140 (MQ=255)

               gAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAgg                                                                                                                <  2:263027/140‑1 (MQ=255)

               gAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAgg                                                                                                                <  1:787502/140‑1 (MQ=255)

               gAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAgg                                                                                                                <  1:764633/140‑1 (MQ=255)

                 aCGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGaa                                                                                                                  >  2:996640/1‑136 (MQ=255)

                 aCGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGaa                                                                                                                  <  1:996640/136‑1 (MQ=255)

                             gCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATg                                                                                                  >  1:199752/1‑140 (MQ=255)

                                tACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAg                                                                                               <  1:132009/140‑1 (MQ=255)

                                  cGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGgc                                                                                             >  1:768709/1‑140 (MQ=255)

                                       gagaTGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGgccagcc                                                                                        <  1:659620/140‑1 (MQ=255)

                                              gTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCAt                                                                                 >  2:468424/1‑140 (MQ=255)

                                                ccACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGa                                                                               >  2:837459/1‑140 (MQ=255)

                                                    gTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGgc                                                                           <  1:468424/140‑1 (MQ=255)

                                                     tttAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCCCGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGgct                                                                          <  2:350269/140‑1 (MQ=255)

                                                        aaaaaTCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCTAGCCACGCCATGAGGgctgct                                                                       <  2:768709/140‑1 (MQ=255)

                                                        aaaaaTCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGgctgct                                                                       >  1:348453/1‑140 (MQ=255)

                                                           aaTCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCa                                                                    <  2:822040/140‑1 (MQ=255)

                                                           aaTCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCa                                                                    <  2:199752/140‑1 (MQ=255)

                                                                     acacTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGaa                                                          <  1:479735/140‑1 (MQ=255)

                                                                          tGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAg                                                     >  2:18949/1‑140 (MQ=255)

                                                                                  cGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAg                                             <  1:470565/140‑1 (MQ=255)

                                                                                         atCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAg                                             >  2:916069/1‑133 (MQ=255)

                                                                                         atCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAg                                             <  1:916069/133‑1 (MQ=255)

                                                                                          tCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCgg                                     <  2:1084158/140‑1 (MQ=255)

                                                                                           cAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGa                                    <  1:531023/140‑1 (MQ=255)

                                                                                            aGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGac                                   <  1:18949/140‑1 (MQ=255)

                                                                                              atatAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACTAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAg                                             <  2:754677/128‑1 (MQ=255)

                                                                                              atatAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAg                                             >  1:754677/1‑128 (MQ=255)

                                                                                                   aaTTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCa                            <  1:888539/140‑1 (MQ=255)

                                                                                                   aaTTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCa                            <  1:837459/140‑1 (MQ=255)

                                                                                                    aTTAGATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCAc                           <  2:482630/140‑1 (MQ=255)

                                                                                                        gATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGc                       >  1:703174/1‑140 (MQ=255)

                                                                                                        gATATATCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGc                       >  1:327594/1‑140 (MQ=255)

                                                                                                         atatatCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCa                      <  2:1085712/140‑1 (MQ=255)

                                                                                                             atCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGaa                  >  1:568167/1‑140 (MQ=255)

                                                                                                              tCTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAac                 >  1:723945/1‑140 (MQ=255)

                                                                                                               cTAATTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAaca                >  2:551420/1‑140 (MQ=255)

                                                                                                                  aTTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATg                    >  1:186928/1‑133 (MQ=255)

                                                                                                                  aTTAAGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATg                    <  2:186928/133‑1 (MQ=255)

                                                                                                                     aaGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCa          <  1:517898/140‑1 (MQ=255)

                                                                                                                      aGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCaa         >  1:800094/1‑140 (MQ=255)

                                                                                                                      aGCAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCaa         >  1:6652/1‑140 (MQ=255)

                                                                                                                        cAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGt            >  2:1052384/1‑135 (MQ=255)

                                                                                                                        cAAAAGGAGGCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGt            <  1:1052384/135‑1 (MQ=255)

                                                                                                                             ggaggCTGATATAAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAGCACGGTCAATGCTGCg  <  2:327594/140‑1 (MQ=255)

CGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGAAGGCCAGCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCG  >  NC_000913/3216644‑3216908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A