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
A16 F20 I40 R1	12	45.4	1473824	96.3%	1419292	148.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	2,870,339	G→A	G134S (GGC→AGC)	iap →	aminopeptidase in alkaline phosphatase isozyme conversion

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,870,339	0	G	A	95.0%	113.4 / NA	40	G134S (GGC→AGC)	iap	aminopeptidase in alkaline phosphatase isozyme conversion
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (18/20); minor base C (2/0); total (20/20)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCGCGATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCGGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGGC  >  CP009273/2870193‑2870482

cccgcGATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTcagc                                                                                                                                               <  1:375913/149‑1 (MQ=255)

        aaTCGTAAGAGCTGGCAAAACGTGGCGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGAc                                                                                                                                       <  1:257678/149‑1 (MQ=255)

              aaGAGCGGGCATAACGTGACGGGAAGTACGGCGATTGCCGCTCCTGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACa                                                                                                                                 <  1:168497/149‑1 (MQ=255)

                   cTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGaa                                                                                                                            >  1:488345/1‑149 (MQ=255)

                   cTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGAGCCGGGGGGAAACGACAATATGGCCACATC‑GGTTACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGTGCTGACGTTACCAGGaa                                                                                                                            >  1:174004/1‑149 (MQ=255)

                      gCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATgg                                                                                                                         >  2:461496/1‑149 (MQ=255)

                      gCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATgg                                                                                                                         >  1:157385/1‑149 (MQ=255)

                       cATGACGGGACGGGAAGGACGGTGATTGCCGCGCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGga                                                                                                                        <  1:671149/149‑1 (MQ=255)

                       cATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACATGGatgtga                                                                                                                        <  2:454870/149‑6 (MQ=255)

                               gACGGGGAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAAcg                                                                                                                <  2:512217/149‑1 (MQ=255)

                                  gggAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGAGCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGAGGCCGATGCCCATCCCCGCGGGCTGACGTTACAAGGGAAGGATGATAGcgccg                                                                                                             >  2:150901/1‑149 (MQ=255)

                                          cGGTGGTTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCCGCGGGCTGAAGTTACAAGGAATGGATGATAACGCCGCAGGTTTa                                                                                                     >  1:175791/1‑149 (MQ=255)

                                           ggTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAg                                                                                                    <  1:513608/149‑1 (MQ=255)

                                               aTTGCCGCTCATGAAGGCAAAGCGCCGCGGCAGATCAGCAGTAGGG‑GGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGGCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGgtgt                                                                                                <  1:424739/149‑1 (MQ=255)

                                                   ccGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATg                                                                                            >  1:253289/1‑149 (MQ=255)

                                                     gCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGCCGTTACAAGGAGTGGATGATCAGGCCGCAGGTTTAGGTGTCATGCt                                                                                          >  1:18194/1‑149 (MQ=255)

                                                         aTGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGaa                                                                                      <  2:582791/149‑1 (MQ=255)

                                                         aTGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGaa                                                                                      >  2:358339/1‑149 (MQ=255)

                                                           gAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGGTGATAACGCCGCAGGTTTAGGGGTCATGCTGGAAtt                                                                                    >  2:448196/1‑149 (MQ=255)

                                                            aaGGCGAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTCCAAGGAATGGCTGCTAAGGGTGACGGATTAGGCGGCATGCTGGAGTTg                                                                                   >  2:515186/1‑149 (MQ=255)

                                                             aGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTgg                                                                                  <  1:190824/149‑1 (MQ=255)

                                                                            gcagATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGaaaa                                                                   <  1:377029/149‑1 (MQ=255)

                                                                                         aTGG‑CGCTTCAGTATACTTACGCCCCTCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGCTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGa                                                      >  2:433447/1‑149 (MQ=255)

                                                                                           gg‑CGCATCTGGCTACTTCCCCCCCGCTGAGCGATGCTGACGCCGATGCCACTCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGt                                                    <  1:458762/149‑1 (MQ=255)

                                                                                           gg‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGt                                                    <  1:458764/149‑1 (MQ=255)

                                                                                                    tGGATACTTACGCCCCGCTGAGCGATGCAGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTCTGGTAtt                                            >  1:442577/1‑149 (MQ=255)

                                                                                                         aCTTACGCCCCGCTGAGCGATGCTGACGCCGACGCCAATCTCAGCGGGCTGAAGATACAAGGCATGGATGATACCGCCGCCGGTTTATGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGAtt                                       <  2:407159/149‑1 (MQ=255)

                                                                                                              ccgcccGCTGTGCGAGGCTGACGCCGATGGCAATCTCAGTGGGCGGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGTAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTgg                                  <  1:642678/146‑1 (MQ=255)

                                                                                                               gCCCCGCTGCGCGATGCTGACGCCGATGCCAACCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGTCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGc                                 <  1:25225/149‑1 (MQ=255)

                                                                                                               gCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGc                                 <  1:461496/149‑1 (MQ=255)

                                                                                                                 cccGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGa                               >  1:361667/1‑149 (MQ=255)

                                                                                                                 cccGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTAACGAGTATGGTATTCGATTTGTGGCGa                               >  1:179986/1‑149 (MQ=255)

                                                                                                                 cccGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTCACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGAAATCGCCGATTGGTTTTAAATTTATGCCTACCGCGTATGGTATTCGATTTGTGGCGa                               >  1:240346/1‑149 (MQ=255)

                                                                                                                         gCGGTGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTGGTGGCGACCAgcggc                       <  2:409219/149‑1 (MQ=255)

                                                                                                                                 gACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGa               >  1:521691/1‑149 (MQ=255)

                                                                                                                                      cGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGCAgggc          >  1:634863/1‑148 (MQ=255)

                                                                                                                                           ccAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTa     >  1:230399/1‑149 (MQ=255)

                                                                                                                                           ccAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTa     <  2:488345/149‑1 (MQ=255)

                                                                                                                                             aaTCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTGATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAACAGAGGGGATATTAgc   >  2:477735/1‑148 (MQ=255)

                                                                                                                                              aTCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGgc  <  2:174004/149‑1 (MQ=255)

                                                                                                                                              aTCTCAGCGGGCTCACGTTACAAGGAACGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTTTGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGTAGGGAAATTAGgc  <  1:527255/149‑1 (MQ=255)

CCCGCGATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGG‑CGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCGGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGGC  >  CP009273/2870193‑2870482

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