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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,687,757	T→C	K207K (AAA→AAG)	fumA ←	fumarate hydratase (fumarase A), aerobic Class I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,687,757	0	T	C	97.1%	119.6 / ‑3.7	35	K207K (AAA→AAG)	fumA	fumarate hydratase (fumarase A), aerobic Class I
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/15); total (19/16)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGT  >  NC_000913/1687613‑1687900

ttCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTcccc                                                                                                                                           >  1:483563/1‑151 (MQ=255)

 tcatcaTAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTcccc                                                                                                                                           <  2:637312/150‑1 (MQ=255)

  catcatAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCg                                                                                                                                          <  1:549391/150‑1 (MQ=255)

  caccatAGTATTTCGCGGCAGACAGTTTCACCGATTTAAGGTCCGCTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATCCGGAGGACAGGCCGCCGTACCCAGCGTGCGCACCTTCTCAACCAGGTAATTTTTCAACTTcccc                                                                                                                                           >  1:651455/4‑149 (MQ=255)

              tCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGc                                                                                                                             >  1:123604/1‑151 (MQ=255)

                         aGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCt                                                                                                                  >  1:553299/1‑151 (MQ=255)

                                  gTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATag                                                                                                             >  1:442715/1‑147 (MQ=255)

                                     ttAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACg                                                                                                      >  1:55081/1‑151 (MQ=255)

                                      tAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt                                                                                                     >  2:116110/1‑151 (MQ=255)

                                        aGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt                                                                                                   <  1:528667/151‑1 (MQ=255)

                                              gTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTg                                                                                             >  1:412327/1‑151 (MQ=255)

                                                   tGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGa                                                                                         >  1:570920/1‑150 (MQ=255)

                                                               accaATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTg                                                                            >  1:34764/1‑151 (MQ=255)

                                                                ccaATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTgg                                                                           >  1:642435/1‑151 (MQ=255)

                                                                     aacgaacgCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATa                                                                      <  2:589240/151‑1 (MQ=255)

                                                                         aacgCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACaga                                                                  <  1:176130/151‑1 (MQ=255)

                                                                         aacgCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACaga                                                                  <  1:523954/151‑1 (MQ=255)

                                                                          acgCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACagag                                                                 <  2:61128/151‑1 (MQ=255)

                                                                                      aCGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtc                                                     <  2:435847/151‑1 (MQ=255)

                                                                                       cGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcg                                                    <  1:193136/151‑1 (MQ=255)

                                                                                         gaggaCAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgtc                                                  <  1:579599/151‑1 (MQ=255)

                                                                                               aGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATc                                            >  1:215701/1‑151 (MQ=255)

                                                                                                  ccgccgTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAAc                                         >  1:301080/1‑151 (MQ=255)

                                                                                                             aGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCAGCGTCAGTAACGCTTTGGTTTCCTGATTTAGATACGTCTTGTTTGCCAAACCACCCCCTTTGACGATACAGAGGAATTTGTGTTCGTCGCCATCAACGTCATAAAgat                              <  1:242352/151‑1 (MQ=255)

                                                                                                              gCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATaa                                  >  2:653487/1‑146 (MQ=255)

                                                                                                              gCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgatc                             <  1:567351/151‑1 (MQ=255)

                                                                                                                  gcgcATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgatcgatc                         <  1:196568/151‑1 (MQ=255)

                                                                                                                   cgcATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCt                        <  1:215042/151‑1 (MQ=255)

                                                                                                                   cgcATCTTCTCAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCt                        >  2:279074/1‑151 (MQ=255)

                                                                                                                          tctcAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTgg                 >  1:614487/1‑151 (MQ=255)

                                                                                                                          tctcAACCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTg                  <  1:514115/150‑1 (MQ=255)

                                                                                                                               aCCAGGTAATTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGc                >  2:83333/1‑147 (MQ=255)

                                                                                                                                       aTTTTTCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCg    <  2:362421/151‑1 (MQ=255)

                                                                                                                                       aTTTTTCAGCTTCCCCGGCGTAAGTAACGCTTTGGCTTCCTGATAGAGCTACGGCTTGTTTGCCGATCCACCACCTTTGGCGATACAGAGGACTTTGTATTCGTCGCCATAAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCg    >  1:245020/1‑151 (MQ=255)

                                                                                                                                         ttttCAGCTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGt  >  2:538867/1‑151 (MQ=255)

TTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCACCAATAACGAACGCAATATGATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGT  >  NC_000913/1687613‑1687900

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A