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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,241,409	T→C	Q87R (CAG→CGG)	galS ←	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,241,409	0	T	C	97.1%	117.7 / ‑3.6	34	Q87R (CAG→CGG)	galS	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (18/15); total (19/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.25e-01

ATCCATAAATTGCGCCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCTGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGCCGATAATCCAGCTCACTCACG  >  NC_000913/2241261‑2241552

aTCCATAAATTGCGCCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGAtgccgc                                                                                                                                               >  1:412303/1‑151 (MQ=255)

      aaaTTGCGCCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGc                                                                                                                                          <  2:359642/150‑1 (MQ=255)

      aaaTTGCGCCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCg                                                                                                                                         <  1:382510/151‑1 (MQ=255)

        aTTGCGCCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGAc                                                                                                                                       >  1:199475/1‑151 (MQ=255)

             gcCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGAt                                                                                                                                  <  2:414546/151‑1 (MQ=255)

                 gTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCAc                                                                                                                              >  2:509738/1‑151 (MQ=255)

                  ttCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATcc                                                                                                                                <  1:490151/148‑1 (MQ=255)

                  ttCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATcc                                                                                                                                >  2:490141/1‑148 (MQ=255)

                    cATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCTGCTGAGCGACCAGATCCACCGc                                                                                                                           >  1:154409/1‑151 (MQ=255)

                       cGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCttt                                                                                                                        >  2:540725/1‑151 (MQ=255)

                         tCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCtttt                                                                                                                       >  2:529780/1‑150 (MQ=255)

                                     tttGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCg                                                                                                           <  1:108229/150‑1 (MQ=255)

                                      ttGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGa                                                                                                          >  1:492818/1‑150 (MQ=255)

                                         aGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGaaaa                                                                                                       >  2:70609/1‑150 (MQ=255)

                                            gAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACg                                                                                                    <  1:142808/150‑1 (MQ=255)

                                                aaTCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCa                                                                                               <  2:323805/151‑1 (MQ=255)

                                                    aaCGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGaa                                                                                            >  1:510589/1‑150 (MQ=255)

                                                      cGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACg                                                                                         <  2:625020/151‑1 (MQ=255)

                                                                     gCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACg                                                                          >  1:435905/1‑151 (MQ=255)

                                                                      cGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGc                                                                         >  2:184722/1‑151 (MQ=255)

                                                                      cGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGc                                                                         >  1:272101/1‑151 (MQ=255)

                                                                       gAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGcc                                                                        >  2:561815/1‑151 (MQ=255)

                                                                       gAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGcc                                                                        <  1:373858/151‑1 (MQ=255)

                                                                           tAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATg                                                                    >  1:218323/1‑151 (MQ=255)

                                                                                       ggCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAAcc                                                        <  2:6525/151‑1 (MQ=255)

                                                                                            gACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGt                                                   <  2:435896/151‑1 (MQ=255)

                                                                                                         cGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTgg                                      >  1:576790/1‑151 (MQ=255)

                                                                                                              cATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGCCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCAtt                                 <  2:44973/151‑1 (MQ=255)

                                                                                                                tGATAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTgg                               >  2:355315/1‑151 (MQ=255)

                                                                                                                  aTAGCTATTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCg                             <  2:191290/151‑1 (MQ=255)

                                                                                                                        aTTGCCGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGc                       <  2:218318/151‑1 (MQ=255)

                                                                                                                            ccGATTAGCACGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGCCGAt                   >  2:546847/1‑151 (MQ=255)

                                                                                                                                     aCGTATTTCTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGCCGAGAATCCAGc           <  2:433705/150‑1 (MQ=255)

                                                                                                                                             cTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGCCGATAATCCAGCTCACTCACg  >  1:50069/1‑151 (MQ=255)

                                                                                                                                             cTGATGCCGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGCCGATAATCCAGCTCACTCACg  >  1:527834/1‑151 (MQ=255)

ATCCATAAATTGCGCCAGTTCATCGTCACTCAATGCTTTTGAGTGAACAATCAACGCATTACAACGCTGGCGAATTAACACCTCAATGGCGTGACGCTCTTTTTCCGCTTCATGATAGCTATTGCCGATTAGCACGTATTTCTGATGCTGCTGAGCGACCAGATCCACCGCTTTTACCAGCGCGCCGAAAAACGCATCAGAAACGTCCATCACCACCACGCCAATGGTGTCGCTAACCTGAGTTGCCAGCGCCTGGGCATTGGCGTTTGGCCGATAATCCAGCTCACTCACG  >  NC_000913/2241261‑2241552

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A