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
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,316,160	G→A	891 (TAG→TAA)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,316,160	0	G	A	97.9%	149.0 / ‑3.5	47	891 (TAG→TAA)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (22/24); minor base T (1/0); total (23/24)
Fisher's exact test for biased strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.89e-01

GTATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAGCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGAC  >  NC_000913/2316026‑2316287

gTATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAg                                                                                                                             <  1:697618/139‑1 (MQ=255)

 tATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                            <  2:51656/139‑1 (MQ=255)

 tATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                            >  1:783665/1‑139 (MQ=255)

     tGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGc                                                                                                                        <  1:86891/139‑1 (MQ=255)

       ccATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCt                                                                                                                      <  2:783665/139‑1 (MQ=255)

          tGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTAtt                                                                                                                   >  2:131076/1‑139 (MQ=255)

            cTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTAc                                                                                                                 >  1:507630/1‑139 (MQ=255)

             tAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACa                                                                                                                <  1:54768/139‑1 (MQ=255)

                aTCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGa                                                                                                             >  2:3994/1‑139 (MQ=255)

                 tCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                            <  2:145048/139‑1 (MQ=255)

                    ggTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACaa                                                                                                         >  1:650626/1‑139 (MQ=255)

                           ggCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAAc                                                                                                  <  1:27171/139‑1 (MQ=255)

                                  aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                           <  2:9512/139‑1 (MQ=255)

                                  aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                           <  2:2545/139‑1 (MQ=255)

                                            aaCGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGa                                                                                 <  1:773054/139‑1 (MQ=255)

                                             aCGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGAc                                                                                <  1:42021/139‑1 (MQ=255)

                                              cGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGAcc                                                                               >  1:142524/1‑139 (MQ=255)

                                               gCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCa                                                                              <  1:706600/139‑1 (MQ=255)

                                                    aaCATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGa                                                                         <  2:29146/139‑1 (MQ=255)

                                                             ttCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGt                                                                >  1:298274/1‑139 (MQ=255)

                                                                 tGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCgg                                                            >  2:68402/1‑139 (MQ=255)

                                                                  gagaAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGt                                                           <  1:3994/139‑1 (MQ=255)

                                                                          tGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaa                                                   >  1:570524/1‑139 (MQ=255)

                                                                          tGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaa                                                   >  1:212800/1‑139 (MQ=255)

                                                                              ccAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCa                                               <  1:301822/139‑1 (MQ=255)

                                                                               cAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCAc                                              <  1:68402/139‑1 (MQ=255)

                                                                                      aGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCa                                       >  1:450099/1‑139 (MQ=255)

                                                                                      aGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCa                                       >  1:667681/1‑139 (MQ=255)

                                                                                        aaaaaTACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTATCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCaaa                                     >  2:196268/1‑139 (MQ=255)

                                                                                             tACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAg                                <  1:383537/139‑1 (MQ=255)

                                                                                             tACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAg                                >  2:518808/1‑139 (MQ=255)

                                                                                                  cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGt                           >  1:315750/1‑139 (MQ=255)

                                                                                                  cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGt                           >  1:168498/1‑139 (MQ=255)

                                                                                                          ttGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAAtgttg                   >  2:142274/1‑139 (MQ=255)

                                                                                                                 ttATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACt                                             >  2:619173/1‑106 (MQ=255)

                                                                                                                 ttATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACt                                             <  1:619173/106‑1 (MQ=255)

                                                                                                                   aTGTCAAGAGCTTGCTGTAACAAGGTAGCTTATTAc                                                                                                                 >  1:284054/1‑36 (MQ=255)

                                                                                                                   aTGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTAc                                                                                                                 <  2:284054/36‑1 (MQ=255)

                                                                                                                      tCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTg       >  2:774210/1‑139 (MQ=255)

                                                                                                                        aaGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGaa     <  2:570524/139‑1 (MQ=255)

                                                                                                                         agagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGaa     <  1:324857/138‑1 (MQ=255)

                                                                                                                         agagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGaa     >  2:324857/1‑138 (MQ=255)

                                                                                                                          gagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGa   <  2:110832/139‑1 (MQ=255)

                                                                                                                          gagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGa   <  2:671646/139‑1 (MQ=255)

                                                                                                                          gagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGa   <  1:400793/139‑1 (MQ=255)

                                                                                                                           agCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGAc  >  1:648104/1‑139 (MQ=255)

                                                                                                                           agCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGAc  >  1:484516/1‑139 (MQ=255)

GTATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAGCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGAC  >  NC_000913/2316026‑2316287

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A