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 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,324,876	A→G	L97P (CTG→CCG)	phnC ←	phosphonate ABC transporter ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,324,876	0	A	G	97.8%	156.6 / NA	45	L97P (CTG→CCG)	phnC	phosphonate ABC transporter ATPase
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (23/21); minor base T (0/1); total (23/22)
Fisher's exact test for biased strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGCCAACGCGGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCAGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGATATGGCTACCGACAGATTTATCGCCGGTAATC  >  NC_000913/4324740‑4325007

cATGCCAACGCGGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCggg                                                                                                                                   <  1:265053/139‑1 (MQ=255)

   gCCAACGCGGTTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCT‑AAACAGGTGCGCCAGAACGGCGTGCTGTCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTgc                                                                                                                               >  2:146826/1‑138 (MQ=255)

   gCCAACGCGGGTCAGCGCCTGTAACGCGCGCTGTGTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGACGTGCTGCCGAGCGCGCCAATCAGCCCGTTCCCCAGTACGCTCAGGCGGTTCACCTGGTTg                                                                                                                                <  2:1080964/139‑1 (MQ=255)

   gCCAACGCGGATCAGCGCCTGTAACACGCGCTGTTTCTCCTCGCCGGTGAACCCGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAACCAGCACGTTCTCCAGTACGATCAGGCGGTTCACCGGGTTg                                                                                                                                <  2:408233/139‑1 (MQ=255)

     cAACGCGGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGaa                                                                                                                              <  1:317279/139‑1 (MQ=255)

     cAACGCGGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGaa                                                                                                                              >  2:317279/1‑139 (MQ=255)

     cAACGCGGGTCAGCGCCTGTAACGCGCGATGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGaa                                                                                                                              >  1:689988/1‑139 (MQ=255)

        cgcgGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttg                                                                                                                           <  1:212975/139‑1 (MQ=255)

        cgcgGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttg                                                                                                                           <  2:554024/139‑1 (MQ=255)

          cgGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttgtt                                                                                                                         <  1:181012/139‑1 (MQ=255)

             gTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAACCAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGa                                                                                                                      >  2:575852/1‑139 (MQ=255)

             gTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGa                                                                                                                      <  2:143502/139‑1 (MQ=255)

              tCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGaa                                                                                                                     >  1:78538/1‑139 (MQ=255)

                    ccTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTa                                                                                                               <  2:21102/139‑1 (MQ=255)

                       gTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttgttg                                                                                                                        <  1:1012871/127‑1 (MQ=255)

                       gTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttgttg                                                                                                                        >  2:1012871/1‑127 (MQ=255)

                            gcgcgcTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTg                                                                                                                                <  2:515512/114‑1 (MQ=255)

                            gcgcgcTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTg                                                                                                                                >  1:515512/1‑114 (MQ=255)

                               cgcTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATggg                                                                                                    >  1:1111557/1‑139 (MQ=255)

                                    tttCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCgg                                                                                               <  2:78538/139‑1 (MQ=255)

                                              ccGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTa                                                                                                               >  1:274225/1‑113 (MQ=255)

                                              ccGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGa                                                                                     <  1:575852/139‑1 (MQ=255)

                                              ccGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGGGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTa                                                                                                               <  2:274225/113‑1 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGTGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGc                                                                                                             <  1:818508/94‑1 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGTGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGc                                                                                                             >  2:818508/1‑94 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCgg                                                                                      >  2:248703/1‑117 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCgg                                                                                      <  1:248703/117‑1 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGc                                                                           >  1:1057277/1‑128 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGc                                                                           <  2:1057277/128‑1 (MQ=255)

                                                                   gTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCtt                                                                >  1:78012/1‑139 (MQ=255)

                                                                       gcCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttg                                                                                                                           <  1:1100148/76‑1 (MQ=255)

                                                                       gcCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAAttg                                                                                                                           >  2:1100148/1‑76 (MQ=255)

                                                                       gcCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTcgcg                                                            <  2:689988/139‑1 (MQ=255)

                                                                                   tgctgcCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCg                                                >  2:520798/1‑139 (MQ=255)

                                                                                     ctgcCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAata                                                                                                                   <  2:274385/70‑1 (MQ=255)

                                                                                     ctgcCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAata                                                                                                                   >  1:274385/1‑70 (MQ=255)

                                                                                      tgcCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCTGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGcc                                             >  2:796613/1‑139 (MQ=255)

                                                                                               cgcCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTc                                    >  1:711090/1‑139 (MQ=255)

                                                                                                   aaTCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGata                                <  1:520798/139‑1 (MQ=255)

                                                                                                         cACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTa                                                                                                               <  1:274924/54‑1 (MQ=255)

                                                                                                         cACGTTCTCCAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTa                                                                                                               >  2:274924/1‑54 (MQ=255)

                                                                                                                 ccAGTACGCTCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGATATGGCTACCGACAGa                  >  1:669656/1‑139 (MQ=255)

                                                                                                                          tCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGATATGGCTACCGACAGATTTATCGcc         >  2:388376/1‑139 (MQ=255)

                                                                                                                          tCAGGCGGTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGATATGGCTACCGACAGATTTATCGcc         >  2:945934/1‑139 (MQ=255)

                                                                                                                                 gTTCACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGATATGGCTACCGACAGATTTATCGCCGGTAATc  >  2:561793/1‑139 (MQ=255)

                                                                                                                                    cACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTc                                    >  1:505756/1‑102 (MQ=255)

                                                                                                                                    cACCGGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTc                                    <  2:505756/102‑1 (MQ=255)

CATGCCAACGCGGGTCAGCGCCTGTAACGCGCGCTGTTTCTGCTCGCCGGTGAACCAGCTAAAACAGGTGCGCCAGAACGGCGTGCTGCCGAGCGCGCCAATCAGCACGTTCTCCAGTACGCTCAGGCGGTTCACCAGGTTGAATTGTTGGAATATGTAGCCGGTATGGGCGCGGCTTTTGCGGATATCGCGGGCCAGGCGGCCTTCGCGCTGGACTGTGCGGCCCAGCAGCTCGATATGGCTACCGACAGATTTATCGCCGGTAATC  >  NC_000913/4324740‑4325007

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A