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
A5 F18 I0 R1	56	11.5	256338	92.4%	236856	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	36,444	C→T	52.2%	R36R (AGG→AGA)	tpn ←	IS431mec transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	36,444	0	C	T	52.2%	‑3.9 / 61.2	48	R36R (AGG→AGA)	tpn	IS431mec transposase
Reads supporting (aligned to +/- strand): ref base C (11/12); new base T (14/11); total (25/23)
Fisher's exact test for biased strand distribution p-value = 7.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGT  >  CP000730/36307‑36570

aTTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGACCCCTCCGGTTGATCGTTGAATGATGAACGTTTACACCACGTTCTCtt                                                                                                                             <  1:93671/141‑1 (MQ=11)

aTTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCtt                                                                                                                             <  2:5521/141‑1 (MQ=11)

aTTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCtt                                                                                                                             <  1:124107/141‑1 (MQ=11)

  tttGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTaa                                                                                                                           <  1:38966/141‑1 (MQ=40)

    tGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAata                                                                                                                         >  2:15983/1‑141 (MQ=11)

     gatatACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAatat                                                                                                                        >  2:42622/5‑141 (MQ=11)

      atatACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATAtt                                                                                                                       >  1:105785/4‑141 (MQ=255)

      atatACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATAtt                                                                                                                       >  1:19703/4‑141 (MQ=11)

          aCGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAg                                                                                                                   <  2:53639/141‑1 (MQ=255)

           cGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGa                                                                                                                  >  1:28490/1‑141 (MQ=21)

            gTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTTTTTTTTTTATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGat                                                                                                                 >  2:99811/1‑141 (MQ=11)

               tcatcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGatata                                                                                                              >  1:124399/1‑141 (MQ=255)

               tcatcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGatata                                                                                                              >  1:124400/1‑141 (MQ=255)

                catcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGatatat                                                                                                             >  2:106289/1‑141 (MQ=40)

                catcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGatatat                                                                                                             >  2:106295/1‑141 (MQ=40)

                 atcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATc                                                                                                            <  1:75595/141‑1 (MQ=255)

                  tcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCa                                                                                                           <  2:104076/141‑1 (MQ=255)

                  tcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCa                                                                                                           <  2:96720/141‑1 (MQ=255)

                   caATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCAc                                                                                                          >  1:70894/1‑141 (MQ=255)

                   caATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCAc                                                                                                          >  2:45533/1‑141 (MQ=255)

                     aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGa                                                                                                        <  1:88695/141‑1 (MQ=255)

                     aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                                        <  1:25959/141‑1 (MQ=21)

                      tACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACTGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATCTTTCAGATATATCACGAt                                                                                                       <  1:62749/141‑1 (MQ=255)

                      tACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGAt                                                                                                       >  1:85686/1‑141 (MQ=255)

                      tACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGAt                                                                                                       <  2:53356/141‑1 (MQ=21)

                      tACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGAt                                                                                                       <  2:110961/141‑1 (MQ=21)

                        cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATag                                                                                                     >  1:26071/1‑140 (MQ=255)

                        cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATaa                                                                                                     >  2:104338/1‑141 (MQ=21)

                        cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGACATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATag                                                                                                     >  1:126400/1‑140 (MQ=255)

                         gCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAAc                                                                                                    <  2:43205/141‑1 (MQ=18)

                          ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATagct                                                                                                   >  2:20314/1‑138 (MQ=11)

                            aTTTGTAATAAGCTTTTTTATTCTTTTGCTTCCAATATAAATACAAAAGGAAATCATATTCTTCAACCCAACGGTAGCCCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCa                                                                                                 <  1:76416/141‑1 (MQ=14)

                             tttGTAATAAGCTTTTTTTTGTTTTTTCTTTCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATTACGATAACTCaa                                                                                                >  2:102996/1‑141 (MQ=11)

                             tttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCaa                                                                                                <  1:52624/141‑1 (MQ=11)

                             tttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCaa                                                                                                >  1:9972/1‑141 (MQ=11)

                              ttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAAt                                                                                               >  2:11331/1‑141 (MQ=11)

                              ttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAAt                                                                                               >  1:62971/1‑141 (MQ=21)

                              ttGTAATAAGCTTTTTNATGCTTTTTCTTNCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAAt                                                                                               >  1:79023/1‑141 (MQ=18)

                                gTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATgc                                                                                             <  1:127299/141‑2 (MQ=11)

                                gTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACAGTTGAATGATGAACGATTACACCACGTGCCCTTAATATTTCAGATATATCACGATAACTCAATGt                                                                                             >  1:57355/1‑141 (MQ=255)

                                 taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAAGTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATgca                                                                                            <  1:100918/141‑3 (MQ=11)

                                         ttttttATGCTTTTTTTTTTTTTTTTTTTACAAAATTGGGGCATATTTTTGAACTCAACGGTAGAGCGTTGAATGATGAGCGTTTACACCACGTTCCCTTAATATTTCAGATATATCATGTTAACTCTTTTTATATCTTAg                                                                                    >  2:27305/1‑141 (MQ=11)

                                                              aaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGt                                                               <  1:74744/141‑1 (MQ=34)

                                                                tatGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTAAAATGTTGAACGTTTACACCACGTGCCCTTAAGACATCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTgc                                                             <  1:69857/139‑2 (MQ=11)

                                                                                              cccAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGa                               <  2:57355/141‑1 (MQ=32)

                                                                                               ccAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaa                              >  2:115614/1‑141 (MQ=32)

                                                                                                                           tttACACCACGTTCCCTTTTTTTTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGt  <  1:33503/141‑1 (MQ=12)

                                                                                                                           tttACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGt  <  2:93703/141‑1 (MQ=32)

ATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGT  >  CP000730/36307‑36570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A