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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,904,478	T→G	42.9%	N539T (AAT→ACT)	treC ←	trehalose‑6‑P hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,904,478	0	T	G	42.9%	12.8 / 74.4	70	N539T (AAT→ACT)	treC	trehalose‑6‑P hydrolase
Reads supporting (aligned to +/- strand): ref base T (26/14); new base G (9/21); total (35/35)
Fisher's exact test for biased strand distribution p-value = 7.40e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

ATTACCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGC  >  minE/2904416‑2904543

aTTACCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATgg                                                             <  1:1182436/69‑1 (MQ=255)

   aacGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCAGTAAATTCATGGcac                                                          >  1:461933/3‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAATGCCGTAAAtt                                                                  >  1:618452/1‑61 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAtt                                                                  >  1:2353292/1‑61 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAtt                                                                  >  1:3265770/1‑61 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:1052824/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:2562055/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:2899975/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:2177944/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:2920128/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:3219283/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:174519/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:170473/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:3355044/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:351514/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:160288/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:578141/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:101764/1‑69 (MQ=255)

   aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                          >  1:1214889/1‑69 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:254015/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:382286/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:976489/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:2752034/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:276873/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:279697/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:938414/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:834121/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:779237/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:296149/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:3118947/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:776951/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:498137/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:3282110/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:2324164/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:1191151/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:1244261/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:1469196/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:16698/66‑1 (MQ=255)

               cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:168339/66‑1 (MQ=255)

                 aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                            >  1:1121701/1‑69 (MQ=255)

                 aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                            >  1:932581/1‑69 (MQ=255)

                 aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                            >  1:3051740/1‑69 (MQ=255)

                 aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                            >  1:2602666/1‑69 (MQ=255)

                 aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                            >  1:2694572/1‑69 (MQ=255)

                   gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                          <  1:1202209/69‑1 (MQ=255)

                   gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                          <  1:2663494/69‑1 (MQ=255)

                   gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                          <  1:519656/69‑1 (MQ=255)

                   gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                          <  1:652555/69‑1 (MQ=255)

                   gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                          <  1:1896624/69‑1 (MQ=255)

                   gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                          <  1:3320356/69‑1 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:2692770/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:1528834/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:3370858/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:1673197/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:2321545/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:3195811/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:1949194/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                       >  1:2144786/1‑69 (MQ=255)

                      ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGctt                                        >  1:1758455/1‑68 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                               <  1:1370039/66‑1 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                               <  1:687468/66‑1 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                               <  1:2461464/66‑1 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                               <  1:1661010/66‑1 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                               <  1:3335019/66‑1 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTa                             >  1:2987456/1‑68 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTa                             >  1:1972808/1‑68 (MQ=255)

                                 accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTa                             >  1:2371386/1‑68 (MQ=255)

                                   caccaGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGc                          >  1:1250643/1‑69 (MQ=255)

                                       aGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                <  1:2882229/43‑1 (MQ=255)

                                                          tAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCcgcg   <  1:2318028/69‑1 (MQ=255)

                                                          tAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCcgcg   <  1:2251286/69‑1 (MQ=255)

                                                            aaTTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCgcgc  >  1:1163344/1‑68 (MQ=255)

                                                            aaTTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCgcgc  >  1:2316415/1‑68 (MQ=255)

ATTACCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGC  >  minE/2904416‑2904543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A