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
A25 F111 I0 R1	33	34.4	1317450	90.1%	1187022	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	461,007	T→G	100%	I707S (ATC→AGC)	lon →	Lon protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	461,007	0	T	G	89.8%	66.0 / ‑2.9	28	I707S (ATC→AGC)	lon	Lon protease
Reads supporting (aligned to +/- strand): ref base T (2/1); new base G (16/8); total (19/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAAAAACGTGACATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCC  >  NC_000913/460865‑461146

gAAACAGGTGACATCCGCGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAt                                                                                                                                              <  1:84610/143‑1 (MQ=255)

gAAAAGCGTGACATCCACGTCCACGCACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAt                                                                                                                                              <  1:403659/143‑1 (MQ=255)

          aCATCCACGTCCGCGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTTC‑Gt                                                                                                                                   <  2:7154/143‑1 (MQ=255)

            aTCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGGGAGAGCACTCGGC‑GTgg                                                                                                                                 >  1:328280/1‑143 (MQ=255)

               cacgtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCa                                                                                                                              <  2:150923/143‑1 (MQ=255)

                gcgtgcacgtACCGGAAGGTGCGACGCGGAAAGCTGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGATGGTTTGTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAg                                                                                                                             <  2:113050/142‑1 (MQ=255)

                             ggAAGGTGCCACGCCCAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCCCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCg                                                                                                                <  1:157437/143‑1 (MQ=255)

                                   tGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGCTCGTGCGGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGtt                                                                                                          >  1:303996/1‑143 (MQ=255)

                                     cGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGC‑GTGGTGAGGTACTGCCGATCGGTGGttgg                                                                                                        >  1:166965/1‑141 (MQ=255)

                                       aCGCCGAAAGATGGTCCGAGTGCCGGTATTGCTCTGTGCACCGCGCTGGCTACTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGGGGTGTgaa                                                                                                      >  1:139446/1‑143 (MQ=255)

                                        caccGAAAGGTGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTgaaa                                                                                                     <  1:248138/141‑1 (MQ=255)

                                           cGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACACGGTTCGGTTCAAGGTGGCGATGCAATAAAAGAGCTGTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTgaaagaa                                                                                                  >  1:448616/1‑143 (MQ=255)

                                             aaaGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACGGGTAACCAGGTTCGTGGCGATGTGGCAATGACCGGTGAGATGACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGGTTGGAAGaaaa                                                                                                >  1:190544/1‑143 (MQ=255)

                                                             ccGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCCATGACCGGTGAGAGCACTCTGC‑GTGGCCAGGTACTGCCGAGCGGAGGTTTGAAAGAAAACCTCCTGGCCGCGCAt                                                                                >  2:272605/1‑143 (MQ=255)

                                                             ccGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTTCTGGCAGCGCAt                                                                                >  1:365139/1‑143 (MQ=255)

                                                              cGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATc                                                                               <  1:566641/143‑1 (MQ=255)

                                                               ggTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGAACTCTGC‑GTGGTCAGGTACCGCCGATCTGTGGTTTGAATGAGAAACTCCTGGCAGCGCATcg                                                                              >  1:333561/1‑143 (MQ=255)

                                                                 tATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGCGCACTCTGC‑CTGGCCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTGCTGGCAGCGCATcgcg                                                                            >  1:336175/1‑143 (MQ=255)

                                                                      cTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCggg                                                                       >  1:595892/1‑143 (MQ=255)

                                                                            gCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGACTaaa                                                                 >  1:319277/1‑143 (MQ=255)

                                                                                 tcgcTGTTTTCTTGCCTGACCGGTAACCCGGTTCGTGACGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGt                                                            <  1:168137/142‑1 (MQ=255)

                                                                                 gcgcTGGTTTCTTGCCTGACCGGTACCCCGCTTCGTGCCGATGTGGCAATGACCGGCGAGAGCACTCTGC‑GTGGGCAGGTCCTGCCGATCGGTGGTTTGAAAGAACACCTCCTGGCAGCGCATCGCGGCGGGATTAAACCAGt                                                            <  1:322289/143‑1 (MQ=255)

                                                                                        tggcatGCCTGAACGGCAGCCCCGTTCGTGCGGATGTGGCAATGACCGGTGAGATCACTCTGC‑GTGGCCAGCTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAAtt                                                     <  2:190544/138‑1 (MQ=255)

                                                                                                 tGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGaa                                            >  1:123839/1‑143 (MQ=255)

                                                                                                            ccGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAACATAAACGCGa                                 >  2:609362/1‑143 (MQ=255)

                                                                                                            ccGGTTCGTGCCGATGTGGCAATGACCGGTGAGA‑CACAAAACGGGGGTCAGGTACTGCCGCTCGGTGGTCTGAAAGAGAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAAGTCCGTACGAAAATACAcggca                                 >  2:537111/1‑140 (MQ=255)

                                                                                                                       cGATGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAgaga                      >  1:401058/1‑143 (MQ=255)

                                                                                                                         aTGTGGCAATGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGCAGAGAtt                    >  1:580539/1‑143 (MQ=255)

                                                                                                                                aaTGACCGGTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGCAGAGATTCCTGACa             >  1:317183/1‑143 (MQ=255)

                                                                                                                                        gTGAGAGCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGCTCGAAAATAAACGCGATCGGGAAGAGATCCCTGACAACGTAAtt     >  2:45671/1‑143 (MQ=255)

                                                                                                                                           agagCACGCTGC‑GGGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGcc  <  1:148257/143‑1 (MQ=255)

GAAAAACGTGACATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGC‑GTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCC  >  NC_000913/460865‑461146

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