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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,717,476	T→C	V56A (GTA→GCA)	ghrB →	glyoxylate/hydroxypyruvate reductase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,717,476	0	T	C	97.5%	144.3 / ‑3.7	40	V56A (GTA→GCA)	ghrB	glyoxylate/hydroxypyruvate reductase B
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (18/21); total (19/21)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

AAAGCCTTACCTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGTAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGTATTAACAGAAACCGTCGCC  >  NC_000913/3717334‑3717621

aaaGCCTTACCTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCg                                                                                                                                           <  2:583225/151‑1 (MQ=255)

 aaGCCTTACCTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGc                                                                                                                                          <  2:315596/151‑1 (MQ=255)

  aGCCTTACCTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCa                                                                                                                                         <  1:528378/151‑1 (MQ=255)

   gCCTTACCTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCAt                                                                                                                                        >  1:250350/1‑151 (MQ=255)

         ccTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTgg                                                                                                                                  <  2:287459/151‑1 (MQ=255)

           tgatgaTTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGa                                                                                                                                 >  1:97765/1‑150 (MQ=255)

            gatgatTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGaaa                                                                                                                               <  2:343319/151‑1 (MQ=255)

                            gCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGTAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCg                                                                                                               >  2:37588/1‑151 (MQ=255)

                             ccTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGt                                                                                                              <  2:307003/151‑1 (MQ=255)

                             ccTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGt                                                                                                              <  2:532212/151‑1 (MQ=255)

                               tGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGa                                                                                                                      <  1:305068/141‑1 (MQ=255)

                               tGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGa                                                                                                                      >  2:305070/1‑141 (MQ=255)

                                 cAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGcc                                                                                                           >  1:164114/1‑150 (MQ=255)

                                   agagCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCcac                                                                                                         >  1:263631/1‑150 (MQ=255)

                                     agCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATc                                                                                                      >  2:57669/1‑151 (MQ=255)

                                       cATTTCACCGTTCACCAGGTGGCATACCTCAGCCCACAAACCGTCGAACAAAACGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATc                                                                                                      >  1:565705/1‑149 (MQ=255)

                                           tCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGa                                                                                                 <  1:405548/150‑1 (MQ=255)

                                                gTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCg                                                                                           >  1:440626/1‑151 (MQ=255)

                                                  tCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGt                                                                                          <  2:190405/150‑1 (MQ=255)

                                                      cAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCt                                                                                     >  1:590960/1‑151 (MQ=255)

                                                                 ccTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAAtttt                                                                          >  1:639396/1‑151 (MQ=255)

                                                                   tCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTg                                                                         >  1:618465/1‑150 (MQ=255)

                                                                            aaaCCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATgc                                                               <  1:334444/151‑1 (MQ=255)

                                                                                   cGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTAc                                                         <  1:546994/150‑1 (MQ=255)

                                                                                   cGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCGCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTAc                                                         <  1:235601/150‑1 (MQ=255)

                                                                                     aaCAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGc                                                      <  2:402350/151‑1 (MQ=255)

                                                                                        aaaaTGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCg                                                   <  2:129576/151‑1 (MQ=255)

                                                                                           aTGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGaaa                                                <  2:177773/151‑1 (MQ=255)

                                                                                            tGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGaaa                                                >  1:630902/1‑150 (MQ=255)

                                                                                               agcaATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAAtt                                            >  1:182300/1‑151 (MQ=255)

                                                                                                gcaATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTc                                           >  2:414612/1‑151 (MQ=255)

                                                                                                     ttttGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTctgct                                       <  2:114106/150‑1 (MQ=255)

                                                                                                                    aGGTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAAcc                       <  2:473664/151‑1 (MQ=255)

                                                                                                                      gTTTACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGt                     <  2:519386/151‑1 (MQ=255)

                                                                                                                        ttACTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGACAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGTAt                   >  2:539739/1‑151 (MQ=255)

                                                                                                                          aCTGGGTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGTAtt                  <  1:522909/150‑1 (MQ=255)

                                                                                                                               gTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGaaa                                                >  2:523130/1‑115 (MQ=255)

                                                                                                                               gTTCAAACGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGaaa                                                <  1:523127/115‑1 (MQ=255)

                                                                                                                                    aaCGAGAATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGTATTAACAGAAACCg       >  2:145023/1‑151 (MQ=255)

                                                                                                                                         gaATGCAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGTATTAACAGAAACCGTCGcc  >  1:628940/1‑151 (MQ=255)

AAAGCCTTACCTGATGATTTACTGCAACGCCTGCAAGAGCATTTCACCGTTCACCAGGTGGCAAACCTCAGCCCACAAACCGTCGAACAAAATGCAGCAATTTTTGCCGAAGCTGAAGGTTTACTGGGTTCAAACGAGAATGTAAATGCCGCATTGCTGGAAAAAATGCCGAAACTGCGTGCCACATCAACGATCTCCGTCGGCTATGACAATTTTGATGTCGATGCGCTTACCGCCCGAAAAATTCTGCTGATGCACACGCCAACCGTATTAACAGAAACCGTCGCC  >  NC_000913/3717334‑3717621

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A