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
A17 F172 I1 R2	29	34.5	745914	96.0%	716077	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	638,614	G→T	T14K (ACA→AAA)	thiD ←	phosphomethylpyrimidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	638,614	0	G	T	96.8%	90.0 / ‑2.6	31	T14K (ACA→AAA)	thiD	phosphomethylpyrimidine kinase
Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (17/13); total (18/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

GGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAAAT  >  CP000730/638485‑638750

ggTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCg                                                                                                                               <  1:186926/141‑1 (MQ=255)

    aTGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTTTCAGAACCGACaa                                                                                                                           >  2:203457/1‑141 (MQ=255)

    aTGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCaa                                                                                                                           >  2:335731/1‑141 (MQ=255)

     tGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAAGCGGCGAt                                                                                                                          >  2:230780/1‑141 (MQ=255)

         gtAGCATCGTGTGACCTTGTATCTTTATCGATAGTAGCGATGGCAGTTAAAGGGACCATGGTATACGTATCGAATTCTTGGAACGTTTTCAAATCTGCTTGCAGACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGtt                                                                                                                      <  2:328178/141‑1 (MQ=255)

         gtAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGtt                                                                                                                      <  2:141002/141‑1 (MQ=255)

              aTCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAAc                                                                                                                 <  2:347999/141‑1 (MQ=255)

              aTCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAAc                                                                                                                 <  2:180234/141‑1 (MQ=255)

              aTCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAAc                                                                                                                 <  2:139762/141‑1 (MQ=255)

                    tgACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAActttctt                                                                                                           >  2:351465/1‑141 (MQ=255)

                       ccATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTaa                                                                                                        >  2:17088/1‑141 (MQ=255)

                        cATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTaaa                                                                                                       >  1:187556/1‑141 (MQ=255)

                              tCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTNTCTAATTNTTGGNACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACNTTCTTTAAANCCAtt                                                                                                 >  2:288226/1‑141 (MQ=255)

                                 ttATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGGACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAg                                                                                              >  2:101038/1‑141 (MQ=255)

                                  tATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGc                                                                                             <  2:219666/141‑1 (MQ=255)

                                  tATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCATGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTACAGCCATTGAGc                                                                                             >  2:166215/1‑141 (MQ=255)

                                    tCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCtt                                                                                           >  1:175762/1‑141 (MQ=255)

                                       aTAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCAc                                                                                        <  2:115681/141‑1 (MQ=255)

                                           tAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCt                                                                                    >  1:40283/1‑141 (MQ=255)

                                                   gCAGTTAAAGCGACCATGCCATGCGAAACGAATACTTGGAACGCCATCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGCACCGGCAATTGTTAAAACTTTCTTTAAAGCCAATGAGCTTCACTCCTACataata                                                                            >  2:303129/1‑141 (MQ=255)

                                                        tAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATAtt                                                                       <  2:304288/141‑1 (MQ=255)

                                                                 cATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATtcatc                                                              >  2:211752/1‑141 (MQ=255)

                                                                       aTACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGCACCGGCAATTGTTAAAACTTTCTTTAAAGCCATCGAGCTTCACTCCTACATAATAATATTGTATTCatcatatca                                                        <  2:183496/141‑1 (MQ=255)

                                                                       aTACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATCGAGCTTCACTCCTACATAATAATATTGTATTCatcatatca                                                        <  2:183510/141‑1 (MQ=255)

                                                                                 aaTTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCt                                              <  2:250827/141‑1 (MQ=255)

                                                                                         gAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGaaa                                      >  2:339180/1‑141 (MQ=255)

                                                                                               tttCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATAtt                                >  2:104792/1‑141 (MQ=255)

                                                                                                 tCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTaa                              <  2:372161/141‑1 (MQ=255)

                                                                                                                        ctatcACTTTTGTCCGGACAGGTACTTGTCAAACCTGTCTTTATAGCCCTGGAGCTTCACTCCTGCATAGAAATATTGTATTCATCATATCATTTTTAACCTAATTGTAAAATATTAAGCATTCCATATTATATGAatgtt       >  2:160753/5‑141 (MQ=255)

                                                                                                                        ccAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGAttgtt       >  1:170352/1‑141 (MQ=255)

                                                                                                                             aCTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAAAt  >  2:52805/1‑141 (MQ=255)

GGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAAAT  >  CP000730/638485‑638750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A