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
A14 F1 I2 R1	774	49.2	2112398	96.9%	2046913	118.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,330,357	+T	coding (1395/1434 nt)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,330,353	1	.	T	97.8%	142.9 / ‑3.5	46	coding (1391/1434 nt)	dacB	D‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (21/24); total (21/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

GCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑TTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAGTCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATC  >  NC_000913/3330225‑3330485

gCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAg                                                                                                                             <  1:75791/139‑1 (MQ=255)

    gggtTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:608057/139‑1 (MQ=255)

    ggggTATATATCCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCTTTTGTGCAATATTTTTCTTGCTATGCAGTATAACCGGCGGATCAGCTTAATCGCTGTATTCCGTTAGTGCTT‑TTTTGAAAGccat                                                                                                                         <  2:634899/139‑3 (MQ=255)

    ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:490234/139‑1 (MQ=255)

    ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  1:679479/139‑1 (MQ=255)

    ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTATGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:816934/139‑1 (MQ=255)

      ggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGttt                                                                                                                       <  2:518970/139‑1 (MQ=255)

       gTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTg                                                                                                                      <  2:551553/139‑1 (MQ=255)

        tatataACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGt                                                                                                                     <  1:630021/139‑1 (MQ=255)

                 tGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGata                                                                                                            <  1:103727/139‑1 (MQ=255)

                 tGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGata                                                                                                            <  2:779228/139‑1 (MQ=255)

                  ggCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCATTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGatat                                                                                                           >  1:662314/1‑139 (MQ=255)

                    cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:582457/123‑1 (MQ=255)

                    cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  1:582457/1‑123 (MQ=255)

                    cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 >  2:997551/1‑131 (MQ=255)

                    cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 <  1:997551/131‑1 (MQ=255)

                    cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATAttt                                                                                                         >  2:221767/1‑139 (MQ=255)

                                    agcgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTaatc                                                                                         <  1:221767/139‑4 (MQ=255)

                                      cgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCG‑TTGTATAAAGATATTTATCAGAACAATTAATCaaa                                                                                      >  2:181521/1‑139 (MQ=255)

                                        agcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAg                                                                                                    >  2:697040/1‑124 (MQ=255)

                                        agcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAg                                                                                                    <  1:697040/124‑1 (MQ=255)

                                        agcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCaaaa                                                                                     >  2:856043/1‑139 (MQ=255)

                                           gggCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGa                                                                                  <  1:2418/139‑1 (MQ=255)

                                              cAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGata                                                                                                            >  2:12942/1‑110 (MQ=255)

                                              cAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGata                                                                                                            <  1:12942/110‑1 (MQ=255)

                                              cAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAc                                                                               >  1:168264/1‑139 (MQ=255)

                                                aCGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAccc                                                                             <  2:662314/139‑1 (MQ=255)

                                                aCGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAccc                                                                             <  2:108217/139‑1 (MQ=255)

                                                       gCGTTTGTGCAATATCTTTCTGGC‑ATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGcac                                                                       <  2:852967/137‑1 (MQ=255)

                                                       gCGTTTGTGCAATATCTTTCTGGC‑ATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGcac                                                                       >  1:852967/1‑137 (MQ=255)

                                                              tgCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCgg                                                               >  2:264127/1‑139 (MQ=255)

                                                                               tATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGAc                                              >  1:20022/1‑139 (MQ=255)

                                                                               tATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGAc                                              >  2:89918/1‑139 (MQ=255)

                                                                               tATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATC‑AAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACa                                             >  1:88515/1‑139 (MQ=255)

                                                                                aTGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACa                                             >  1:500539/1‑139 (MQ=255)

                                                                                 tGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACaa                                            <  1:30514/139‑1 (MQ=255)

                                                                                           ccTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTCATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAg                                          >  2:911682/1‑131 (MQ=255)

                                                                                           ccTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAg                                          <  1:911682/131‑1 (MQ=255)

                                                                                           ccTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCttt                                  >  2:956062/1‑139 (MQ=255)

                                                                                              gCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGtt                               >  1:259085/1‑139 (MQ=255)

                                                                                                ggATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTa                             >  1:308747/1‑139 (MQ=255)

                                                                                                                cGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTa             >  1:834520/1‑139 (MQ=255)

                                                                                                                 gTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTaa            <  2:834520/139‑1 (MQ=255)

                                                                                                                  tATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTaaa           <  2:168264/139‑1 (MQ=255)

                                                                                                                         ttAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTa    >  1:151389/1‑139 (MQ=255)

                                                                                                                           aGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATc  <  2:259085/139‑1 (MQ=255)

GCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑TTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAGTCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATC  >  NC_000913/3330225‑3330485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A