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
A7 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	355,466	G→A	100%	P412S (CCA→TCA)	brnQ1 ←	LIVCS family branched chain amino acid:cation symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	355,466	0	G	A	95.9%	106.7 / ‑3.4	39	P412S (CCA→TCA)	brnQ1	LIVCS family branched chain amino acid:cation symporter
Reads supporting (aligned to +/- strand): ref base G (2/0); new base A (21/15); total (24/15)
Fisher's exact test for biased strand distribution p-value = 5.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-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.

GAATTTCATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGATAG  >  CP000730/355331‑355602

gAATTTCATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGCTAATAGCAAAGAGCATGGATGATaaaa                                                                                                                                     >  2:440105/1‑141 (MQ=255)

   tttCATATAAAAAATCCTAGTAATGATGTGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATAcaagcc                                                                                                                                  <  2:571644/141‑1 (MQ=255)

       atatAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATAcaagccaagc                                                                                                                              >  1:476334/1‑141 (MQ=255)

       atatAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATAcaagccaagc                                                                                                                              <  2:468765/141‑1 (MQ=255)

          taAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTaa                                                                                                                           >  2:355130/1‑141 (MQ=255)

            aaaaaGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGCTTCGGACGGCGTAGAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCAAAAt                                                                                                                         >  2:83414/1‑141 (MQ=255)

               aaGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGa                                                                                                                      <  2:354295/141‑1 (MQ=255)

                   cTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGAAGGCGAATAAATACAACGATTATGAAACCGAGAATAGCAAAGAGCATGAATGAGACAAGCCAATCTAAATCAATATc                                                                                                                  >  2:392904/1‑141 (MQ=255)

                    tAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCt                                                                                                                 <  2:327303/141‑1 (MQ=255)

                    tAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGAATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATcagtatag                                                                                                                 >  2:69657/1‑134 (MQ=255)

                    tAGTAACGATGGGTCAAGCATTACTGGGAAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAGTACATCGATTATGAAACCGATAATAGCACCGCACCTGAACACTACAACGCAAGCTAAGTCGATAACt                                                                                                                 >  1:217161/1‑141 (MQ=255)

                      gTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATAAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAACGATACAAGCCCAGCTAAATCGAAAACTGc                                                                                                               >  2:294967/1‑141 (MQ=255)

                               ggTCAATCATTACTAGGCAGTGAGTATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTaa                                                                                                      >  2:208743/1‑141 (MQ=255)

                               ggTCAATCATTACTAGGCAGTGAGCATTTTTTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTaa                                                                                                      <  2:445756/141‑1 (MQ=255)

                                  cAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAAACGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATAGATATCTGCTAAAGGTAAcat                                                                                                   >  2:66571/1‑141 (MQ=255)

                                  cAACCATTACTAGGCAGTAAGCATTTATTAAGTGGTCGCTTGTTTCGGACGGCGTATAAATACACCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAAcat                                                                                                   <  1:4015/141‑1 (MQ=255)

                                   aaTCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAAcatc                                                                                                  >  2:196676/1‑141 (MQ=255)

                                          aCTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTACAGGTAAAATCATaaaag                                                                                           >  2:136130/1‑139 (MQ=255)

                                          aCTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACg                                                                                           <  1:139533/141‑1 (MQ=255)

                                                  gTGAGCACTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCaaa                                                                                   >  1:359386/1‑141 (MQ=255)

                                                      gCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATAAAACGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATAGATATCTGCTAAAGGTAACATCAAAACCGacgccaaaagaa                                                                               >  1:479697/1‑130 (MQ=255)

                                                                 gTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGtaat                                                                    <  1:208743/141‑1 (MQ=255)

                                                                     tCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGt                                                                >  2:50004/1‑141 (MQ=255)

                                                                      cGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGtt                                                               >  1:15646/1‑141 (MQ=255)

                                                                         ttGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGaa                                                            >  2:452877/1‑141 (MQ=255)

                                                                             ttCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTa                                                        <  1:452877/141‑1 (MQ=255)

                                                                             ttCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAAAGCATGAATGATACAAGCCAAGCTAAATAGATATCTGATAAAGGTAACATCATAAAAGATTTCAAAATAACCCCGTGTAATAATTTTAAACTa                                                        >  2:461815/1‑141 (MQ=255)

                                                                                ggACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTGAAAGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTAttt                                                     >  1:131753/1‑141 (MQ=255)

                                                                                 gACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACAACGTGTAATAAGTTGAAACTATTTa                                                    >  1:35695/1‑141 (MQ=255)

                                                                                                           aaaCCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAAt                          <  2:13248/141‑1 (MQ=255)

                                                                                                             aCCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGt                        <  1:165432/141‑1 (MQ=255)

                                                                                                             aCCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGt                        <  1:47519/141‑1 (MQ=255)

                                                                                                                     taGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAg                >  2:193862/1‑141 (MQ=255)

                                                                                                                         aaaGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTACTAAAGGTAACATGATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATCGAAATAATCAATGTAATAACAGTTga            >  2:490046/1‑140 (MQ=255)

                                                                                                                          aaGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCg           <  2:155639/141‑1 (MQ=255)

                                                                                                                          aaGAGCATGAATGATACAAGCCAAGCTAAATCCATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCg           <  1:194604/141‑1 (MQ=255)

                                                                                                                             gacATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACCATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGt        <  1:203407/139‑1 (MQ=255)

                                                                                                                                  gAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGCCGATa   >  1:62966/1‑141 (MQ=255)

                                                                                                                                   aaTGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAAGACCGTGTAATAAGTTGAAACGATTTAGTATTTGTAAAATTGAAATAATCAATGTAATACTAGTTGCGAGTCGTTAg  >  2:350057/1‑141 (MQ=255)

GAATTTCATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGATAG  >  CP000730/355331‑355602

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A