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
A4 F73 I1 R1	27	19.6	661800	98.9%	654520	139.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,834,011	G→T	A34S (GCC→TCC)	norW →	NADH:flavorubredoxin reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,834,011	0	G	T	95.0%	58.8 / ‑2.3	20	A34S (GCC→TCC)	norW	NADH:flavorubredoxin reductase
Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (10/9); total (11/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.56e-01

AGACGTCTTTGAAGAACTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTGCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGTTTAATCTGCACCTGTTTCCACAAA  >  NC_000913/2833879‑2834146

aGACGTCTTTGAAGAACTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGa                                                                                                                                  <  2:227550/140‑1 (MQ=255)

  aCGTCTTTGAAGAACTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACa                                                                                                                                <  2:120041/140‑1 (MQ=255)

       ttcgaagaaCTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATg                                                                                                                           >  1:262686/4‑140 (MQ=255)

          gaagaaCTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGAt                                                                                                                        <  1:167187/140‑1 (MQ=255)

             gaaCTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAg                                                                                                                     <  2:316137/140‑1 (MQ=255)

             gaaCTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAg                                                                                                                     <  2:142729/140‑1 (MQ=255)

                              aaaaTGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCt                                                                                                    <  1:168935/140‑1 (MQ=255)

                                  tGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGc                                                                                                <  2:2468/140‑1 (MQ=255)

                                      tAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATg                                                                                            >  1:139090/1‑140 (MQ=255)

                                      aaaCGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATg                                                                                            >  2:293037/2‑140 (MQ=255)

                                                                    cgccgcCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGAcc                                                              >  2:191313/1‑140 (MQ=255)

                                                                     gccgccCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCt                                                             >  2:25/1‑140 (MQ=255)

                                                                         cccgccAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTAcc                                                         >  1:34724/1‑140 (MQ=255)

                                                                                      gAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGAcggcgg                                            <  2:90604/140‑1 (MQ=255)

                                                                                                      cAGGACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCa                            >  1:134432/1‑140 (MQ=255)

                                                                                                        ggACGCCACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGt                          >  2:265233/1‑140 (MQ=255)

                                                                                                             ccACTATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGTTTAAt                     <  1:25/140‑1 (MQ=255)

                                                                                                                 tATTCCATTAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGTTTAATCTGc                 >  1:112181/1‑140 (MQ=255)

                                                                                                                        ttAACCCTGATTTCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGTTTAATCTGCACCTGtt          >  1:215368/1‑140 (MQ=255)

                                                                                                                                gATTGCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGTTTAATCTGCACCTGTTTCCACaaa  >  1:6441/1‑140 (MQ=255)

AGACGTCTTTGAAGAACTGGCATCGGAGGCAAAATGAGTAACGGCATTGTGATCATCGGTTCGGGCTTCGCCGCCCGCCAACTGGTGAAAAATATTCGCAAACAGGACGCCACTATTCCATTAACCCTGATTGCCGCCGACAGCATGGATGAGTACAACAAACCTGACCTCAGCCATGTTATCAGTCAGGGGCAACGTGCCGATGACCTTACCCGCCAGACGGCGGGTGAATTTGCCGAGCAGTTTAATCTGCACCTGTTTCCACAAA  >  NC_000913/2833879‑2834146

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A