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
A21 F97 I0 R1	51	42.6	1617048	90.7%	1466662	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	461,010	C→A	100%	T708N (ACT→AAT)	lon →	Lon protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	461,010	0	C	A	98.0%	131.7 / ‑5.5	45	T708N (ACT→AAT)	lon	Lon protease
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (18/26); minor base T (1/0); total (19/26)
Fisher's exact test for biased strand distribution p-value = 4.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.37e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGA  >  NC_000913/460876‑461148

actccacgtccacgTGCCGGAAGGGGCGACGCCGAAAGATGGTCGGGGTGCCGGTATTGCTATGTGCACCGCGCTGGTGTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTg                                                                                                                                    <  2:290771/141‑1 (MQ=255)

                  ggAAGGGGCGTGGCCGAGAGATGGTCCGAGTGCCGGTATTGCTATGTGCCCCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTGGTGGCGATGTGGCAATGACCGGTGAGATCAATTTGCGTGGTCAGGTACTGCCGATCg                                                                                                                  <  2:621953/143‑1 (MQ=255)

                   gAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCgg                                                                                                                 >  2:189112/1‑143 (MQ=255)

                     aGGGGCGACGCCGAAAGATGTTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCggtg                                                                                                               <  1:715757/143‑1 (MQ=255)

                         gtggcgcgGAACGATGGTCCGCGTGCCGGTATTGCTTTGTGCTCCGGGCTGGCGTCTGGCCCGACCGGTAACCCGGTTCGTGCCGCTGTGGCAATGCCCGGTGAGATCAATCTGTGTGGTCAGGTACTGCCGATCGGTGGttt                                                                                                           <  2:700799/139‑1 (MQ=255)

                              gCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGCTCGGGGGTTTgaaag                                                                                                      >  2:452111/1‑143 (MQ=255)

                               ccGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACAGATGAGATCATTCTTCGTGGTCAGGTACTGGCGATAGGTGGTTTgaaaga                                                                                                     >  1:670200/1‑143 (MQ=255)

                                  aaaGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGCGGTTTgaaagaaga                                                                                                  >  1:726650/1‑141 (MQ=255)

                                   aaGATGGGCCGAGTGCCGGTATTGCTATGTGCTCCGCGCTGGTTTCGTGCCTGACCGGTAACCCGGTTCGTGCTGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGaaaaa                                                                                                 <  2:278552/143‑1 (MQ=255)

                                          tCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGCGGTCAGGTACTGCCGAGCGGTGGTTCGAAAGACAACCTCCTgg                                                                                          >  2:37247/1‑143 (MQ=255)

                                            cGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCCTACTATCGCACTGCCGATCGGTGGTTTGAAAGAAAAACTCCAGGcc                                                                                        >  2:568164/1‑142 (MQ=255)

                                              agggCCGTTATTGCTATGTGCACCGCGCTGCTTTCTTTCCTGACCTGTAACTCTGCTCGTATAATTGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAATCTCCTGGCAgc                                                                                      <  2:199046/140‑1 (MQ=255)

                                              aGTGCCGGTAGTGCTATGTGCACCGAGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTTGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAgc                                                                                      <  2:59318/143‑1 (MQ=255)

                                                  ccGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCAt                                                                                  <  1:619535/143‑1 (MQ=255)

                                                  ccGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCAt                                                                                  >  2:226920/1‑143 (MQ=255)

                                                        ttGCTATGTGCACCGCGCTGGTTTCTTGCCTAACCGGTAACCCGGTGCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGCTTGAAGGAAAAAGTACTTGCAGCGCATCgcggc                                                                            >  2:184351/1‑143 (MQ=255)

                                                         tGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCgcggcg                                                                           >  1:798738/1‑143 (MQ=255)

                                                             aggtgCACCGCGCTGGTTTCTTGCCGGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGGCCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGAt                                                                       <  2:338887/141‑1 (MQ=255)

                                                             aTGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGAt                                                                       <  2:338883/143‑1 (MQ=255)

                                                                  cACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTaaaa                                                                  <  1:365208/143‑1 (MQ=255)

                                                                    ccGCGCTGGTTGCTCGCCTGACTGGTGAGCCGGTTCGTGCCGATGTGGCAAAGGCCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTAGTTTGCACCGACTTTACCTTCCTGCGCATCGCGGCGGGATTAAAACa                                                                <  2:445100/143‑1 (MQ=255)

                                                                          tGGTGTCGTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTa                                                          >  1:188757/1‑143 (MQ=255)

                                                                              ttCTTGCCTGACCGGTAACCCGGTGCGTGCCGGTGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTc                                                      <  2:386570/143‑1 (MQ=255)

                                                                                  tGCCTGGCCGGTAACCGGGTTCGGGCCGATGTGGCAATGACCGGGGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGtt                                                  <  2:104819/143‑1 (MQ=255)

                                                                                  gggcgggccGGGAGCCCGGTTCGGGCCGATGGGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGtt                                                  <  2:185236/136‑1 (MQ=255)

                                                                                      tGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTGATTCCGTTCgca                                              >  1:494092/1‑141 (MQ=255)

                                                                                      tGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCCGTCGTTTGATCGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGaa                                              <  2:572651/143‑1 (MQ=255)

                                                                                         ccGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAAt                                           >  1:79579/1‑143 (MQ=255)

                                                                                          cGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATa                                          >  1:740037/1‑143 (MQ=255)

                                                                                             gactccGGTTCGTGCCGATGTGGCAATGAGCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAGCTCCTCGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAAGTCCGTTCGAAAATAAAc                                       <  2:502135/139‑1 (MQ=255)

                                                                                             cgaCCCGGTTCGTGGCTGGGTGGCAAGGAATGGTGAGAGCGATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAATCGCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAAc                                       <  2:326156/141‑1 (MQ=255)

                                                                                              aaCCCGGTTCGTGCCGATGTGGCAGTGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTTAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAAcg                                      <  1:412797/143‑1 (MQ=255)

                                                                                               tccgggTTCGTGACGATGTGGCAATGGTCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGAGCGGTGGGTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAAcgc                                     <  1:389158/139‑1 (MQ=255)

                                                                                                            cGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATAAAAACAGTGCTAATTCCGTTCGAAAGTCAACGCGATCTGGAAgaga                        >  2:368235/1‑143 (MQ=255)

                                                                                                               ggtgGCAATGACCGGTTGGATCGATCTGCGTGGTCAGGTGCTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTc                     <  2:103185/142‑1 (MQ=255)

                                                                                                                 tgGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCt                   >  1:715453/1‑143 (MQ=255)

                                                                                                                    cAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGa                 <  2:35146/142‑1 (MQ=255)

                                                                                                                    cAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGa                 >  1:35146/1‑142 (MQ=255)

                                                                                                                      aggACCGGTGAGATCAATCGGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAACCTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACaa              <  1:708028/141‑1 (MQ=255)

                                                                                                                           cGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCCGGCAGAGCTTCCTGACAACGTaa         >  2:275570/1‑143 (MQ=255)

                                                                                                                           cGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCCCGGCGGGATTAAAACACTGCTAATTCCGTTCGACAATACACGCGATCTGGAAGACATTCCTGACCACGTaa         >  2:307862/1‑143 (MQ=255)

                                                                                                                           cGGTGAGATCAATCTGCGTGGCCAGGAACTGCATAGCGCTTTTTTGATAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTaa         <  1:759795/143‑1 (MQ=255)

                                                                                                                             gTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAAtt       <  1:226920/143‑1 (MQ=255)

                                                                                                                               gagaTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGc     <  1:684693/143‑1 (MQ=255)

                                                                                                                                  aTCAATCTGCGTGGTCAGGTACTGCCGATGGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAAGAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGa  >  2:495570/1‑143 (MQ=255)

CATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGA  >  NC_000913/460876‑461148

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A