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
A12 F28 I1 R1	176	31.5	1082462	98.8%	1069472	138.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,106,787	T→C	C358C (TGT→TGC)	nupG →	nucleoside:H(+) symporter NupG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,106,787	0	T	C	97.2%	123.6 / ‑4.1	36	C358C (TGT→TGC)	nupG	nucleoside:H(+) symporter NupG
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (16/19); total (17/19)
Fisher's exact test for biased strand distribution p-value = 4.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

TCGATGATCGTTTACGGTTGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGTATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGATGTTCA  >  NC_000913/3106653‑3106920

tCGATGATCGTTTACGGTTGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCt                                                                                                                                  >  1:329062/1‑140 (MQ=255)

       tCGTTTACGGTTGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCggcggc                                                                                                                           >  2:137433/1‑140 (MQ=255)

          tttACGGTTGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATc                                                                                                                        >  1:90992/1‑140 (MQ=255)

            tACGGTTGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGt                                                                                                                      <  1:74946/140‑1 (MQ=255)

                  tGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCgg                                                                                                                <  1:137433/140‑1 (MQ=255)

                    cgcATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTa                                                                                                              >  2:234353/1‑140 (MQ=255)

                    cgcATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTa                                                                                                              >  1:8775/1‑140 (MQ=255)

                    cgcATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTa                                                                                                              <  2:290373/140‑1 (MQ=255)

                    cgcATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTa                                                                                                              <  2:468984/140‑1 (MQ=255)

                    cgcATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTa                                                                                                              >  2:62024/1‑140 (MQ=255)

                       aTTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAg                                                                                                           <  1:62024/140‑1 (MQ=255)

                                   cAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGt                                                                                               <  2:8775/140‑1 (MQ=255)

                                                tCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGACGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACgg                                                                                  >  1:22031/1‑140 (MQ=255)

                                                    tgtTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCAtt                                                                              >  1:280430/1‑140 (MQ=255)

                                                     gtTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTa                                                                             <  2:231346/140‑1 (MQ=255)

                                                      tttGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGTATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTAc                                                                            >  2:158458/1‑140 (MQ=255)

                                                       ttGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTAcc                                                                           <  1:96122/140‑1 (MQ=255)

                                                              aaaaGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGc                                                                    >  2:31432/1‑140 (MQ=255)

                                                               aaaGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCa                                                                   <  1:344536/140‑1 (MQ=255)

                                                               aaaGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCa                                                                   <  1:31432/140‑1 (MQ=255)

                                                                 agaagTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGa                                                                 <  1:234353/140‑1 (MQ=255)

                                                                    agTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCg                                                              >  2:24997/1‑140 (MQ=255)

                                                                              gCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGAATGGCAGACCGTATGGTTGAt                                                    <  2:280430/140‑1 (MQ=255)

                                                                                        ccAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGt                                          <  2:147860/140‑1 (MQ=255)

                                                                                               acaAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCg                                   <  2:180027/140‑1 (MQ=255)

                                                                                                     gATGTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTc                             >  1:227033/1‑140 (MQ=255)

                                                                                                        gTTCCTGATGATGACTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTgg                          >  2:67645/1‑140 (MQ=255)

                                                                                                              gatgatgaCTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCg                                   >  1:526582/1‑125 (MQ=255)

                                                                                                              gatgatgaCTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCg                                   <  2:526582/125‑1 (MQ=255)

                                                                                                              gatgatgaCTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTg                           >  1:435237/1‑133 (MQ=255)

                                                                                                              gatgatgaCTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTg                           <  2:435237/133‑1 (MQ=255)

                                                                                                                  atgaCTAACGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGtt                <  2:227033/140‑1 (MQ=255)

                                                                                                                          cGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGa        >  1:118420/1‑140 (MQ=255)

                                                                                                                          cGGCTTCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGa        <  2:329062/140‑1 (MQ=255)

                                                                                                                              ttCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGATGtt    >  1:203362/1‑140 (MQ=255)

                                                                                                                              ttCGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGATGtt    <  1:10515/140‑1 (MQ=255)

                                                                                                                                cGGCTGCATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGATGTTCa  <  1:367941/140‑1 (MQ=255)

TCGATGATCGTTTACGGTTGCGCATTCGACTTCTTCAACATCTCTGGTTCGGTGTTTGTCGAAAAAGAAGTTAGCCCGGCAATTCGCGCCAGTGCACAAGGGATGTTCCTGATGATGACTAACGGCTTCGGCTGTATCCTCGGCGGCATCGTGAGCGGTAAAGTTGTTGAGATGTACACCCAAAACGGCATTACCGACTGGCAGACCGTATGGTTGATTTTCGCTGGTTACTCCGTGGTTCTGGCCTTCGCGTTCATGGCGATGTTCA  >  NC_000913/3106653‑3106920

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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