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
A19 F106 I1 R1	24	58.2	1363720	92.2%	1257349	135.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,105,994	T→C	T12T (ACT→ACC)	pdhD →	dihydrolipoyl dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,105,994	0	T	C	94.7%	110.8 / ‑4.1	38	T12T (ACT→ACC)	pdhD	dihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (22/14); minor base A (2/0); total (24/14)
Fisher's exact test for biased strand distribution p-value = 5.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

ATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTC  >  CP000730/1105872‑1106122

aTTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGa                                                                                                                      <  1:414968/135‑1 (MQ=255)

    aTGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAg                                                                                                                  <  1:587229/135‑1 (MQ=255)

        ttcAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGATATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTcc                                                                                                              <  2:212326/133‑1 (MQ=255)

          cAACTGGCCAAAATGCAAGGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGTGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTACTCgctgccaatgcgg                                                                                                            <  2:118287/135‑13 (MQ=255)

                  cAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATAc                                                                                                    >  1:426978/1‑135 (MQ=255)

                    aaaTGCAATGAATCACATTAAACGTTTATTAAAGAATCCCCAATTATCATTAATGGAGGGGTAAAACATGGTAGCTGGAGATTTCCCCATTGAAACACATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGt                                                                                                  <  2:250289/135‑1 (MQ=255)

                                  acaTTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTTAAACAGATACCATAGTAATCGGAGCAGTTCCTGGTGGATACGTTGCAGCAATTCGTg                                                                                    <  2:45115/135‑1 (MQ=255)

                                  acaGTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTg                                                                                    <  2:174008/135‑1 (MQ=255)

                                   caTTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGCGCATCAGTTGCAGCAATACGTGc                                                                                   >  2:11157/1‑135 (MQ=255)

                                   caTTAAACGTTTATTAAATAATCCAGAATTACTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACGGATACCGAAGTAATGGGGGCAGGGCCTGGGGGATACGTTGCAGAAATTCGTGc                                                                                   >  2:665550/1‑135 (MQ=255)

                                               attaAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAgg                                                                       >  2:358839/1‑135 (MQ=255)

                                               attaAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTAGGAGATTTCACAATTGAAACAGATACCATAGGAATCGGAGCAGGTCCTGGTGCATACGTTGCAGCAATTCGTGCAGACCAAttgag                                                                       >  2:176835/1‑132 (MQ=255)

                                                      aatCCATAATTATTATTAAGGGAGGGGTAAAACATTGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTTCTGGTGGATACGTTGCAGCAATTTGTGCAGCTCAATTAGGACaaaaa                                                                <  1:42494/135‑1 (MQ=255)

                                                      aatCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTTTTGCAGCTCAATTAGGACaaaaa                                                                <  1:30591/135‑1 (MQ=255)

                                                      aatCCAGAATGAGTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTGCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACaaaaa                                                                <  2:410796/135‑1 (MQ=255)

                                                                 attattaATGGAGGAGAAAAACATGGTAGATGGAGATTTCAAAATTGCAACAGATAGAATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGAAAAAAAAGAAACAATCGt                                                     >  2:537388/1‑135 (MQ=255)

                                                                    attaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACATTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTga                                                  >  2:241203/1‑135 (MQ=255)

                                                                       aaTGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTCAGaa                                               >  2:452988/1‑135 (MQ=255)

                                                                              gggTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAAt                                        <  1:647465/135‑1 (MQ=255)

                                                                                    aaCATGGTAGTTGGAGATTTCCCAATTAAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggt                                  >  1:599467/1‑135 (MQ=255)

                                                                                     aCATGGTCGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATATtggtg                                 >  1:653093/1‑135 (MQ=255)

                                                                                     aCATGGTCGTTGGAGATTTCCCAATTGAAAAAGATAACATAGTAATCGGAGCCGGGCCTGGTGGATAAGTTGCAGCAATTCGTGCAGCTCAATTAGGACAACAAGTAACAATCGTTGAGAAAgtgaatatagatg                                 >  2:481894/1‑123 (MQ=255)

                                                                                     aCATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtg                                 >  2:44653/1‑135 (MQ=255)

                                                                                     aCATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtg                                 >  1:653128/1‑135 (MQ=255)

                                                                                     aCATGGTAGTTGGAGATGTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtg                                 >  2:457839/1‑135 (MQ=255)

                                                                                      cATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTATGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                >  2:343710/1‑135 (MQ=255)

                                                                                      cATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                >  1:590371/1‑135 (MQ=255)

                                                                                        tGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGGAACCTtgggcgtg                              >  2:201425/1‑130 (MQ=255)

                                                                                           tAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGttt                           >  2:535217/1‑135 (MQ=255)

                                                                                            aGTTGGAGATTTCCCAATTAAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATTGTTGAGAAAGGTAATCTTGGTGGTGTTTg                          <  1:333807/135‑1 (MQ=255)

                                                                                             gTTGGAGATTTTCCAATTGAAACAGATAACATAGGAATCGGAGCAGGTCCTCGGGGATACGTTGCAGCAATTCGTGTAGCGCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGCTAATCTTGGTGGTGTTTGc                         <  2:16909/135‑1 (MQ=255)

                                                                                                           aaTTGAAAAAGATACAATAGTAATCGGAGAAGGTCCGGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGATAAAAAGTAACAATAGTTGAGAAAGCTAATCTTTTTGATGTTTGATTAAACGTAGAAtt           >  2:633127/1‑134 (MQ=255)

                                                                                                            aTTGCAACAGATACCATAGTAATCGGAACAGAACCAAGTGAATACGTTGCAGCAATACGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGt          >  1:76262/1‑135 (MQ=255)

                                                                                                            aTTGAAACAGATACCATAGTAATGGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGt          >  1:365535/1‑135 (MQ=255)

                                                                                                            aTTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGt          >  2:408365/1‑135 (MQ=255)

                                                                                                              tgaccgaGAAACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGAAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGAAATCGTTGCGGTGTTGGCTTAAACGAAGGATGTAt        >  2:117929/7‑135 (MQ=255)

                                                                                                                aaaCAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGGCTTAACGTAGGATGTATTc      <  1:670837/135‑1 (MQ=255)

                                                                                                                    aGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTc  >  2:137817/1‑135 (MQ=255)

ATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTC  >  CP000730/1105872‑1106122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A