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	2,950,748	G→A	52.7%	R82Q (CGG→CAG)	bglJ →	DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,950,748	0	G	A	52.7%	0.3 / 64.8	74	R82Q (CGG→CAG)	bglJ	DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (20/15); new base A (21/18); total (41/33)
Fisher's exact test for biased strand distribution p-value = 8.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01

TGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAC  >  minE/2950683‑2950805

tgaACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCt                                                        <  1:1577223/69‑1 (MQ=255)

    cTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCgg                                                          >  1:407695/1‑63 (MQ=255)

    cTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGAtt                                                    >  1:2778173/1‑69 (MQ=255)

    cTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGAtt                                                    >  1:1179409/1‑69 (MQ=255)

    cTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGAtt                                                    >  1:3329998/1‑69 (MQ=255)

      ggCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTg                                                   >  1:456586/1‑68 (MQ=255)

         gATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTc                                               <  1:1653203/69‑1 (MQ=255)

            tAAGTTTCCGCGTACCCGGAGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTc                                               <  1:794202/66‑1 (MQ=255)

             aaGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCt                                                        <  1:645576/56‑1 (MQ=255)

                 ttCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGc                                       <  1:833862/69‑1 (MQ=255)

                 ttCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGc                                       <  1:1837197/69‑1 (MQ=255)

                  tCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGc                                       >  1:2295433/1‑68 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:3320712/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:3316659/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:3208869/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:3198928/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:3097719/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:2910461/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:2875059/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:63657/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:1056920/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:2255361/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:1822947/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:19104/1‑69 (MQ=255)

                                   tAGTTATTGCGGATGATGATATTGAAGCTCGGATGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg                     >  1:109736/1‑69 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              <  1:461389/39‑1 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              <  1:3157470/39‑1 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              <  1:3161576/39‑1 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              >  1:1685162/1‑39 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              <  1:1662340/39‑1 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              >  1:2699160/1‑39 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              <  1:505083/39‑1 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                                              <  1:679039/39‑1 (MQ=255)

                                        aTTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACgg                       <  1:1913198/62‑1 (MQ=255)

                                                 gatgatATTTAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1577337/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1373399/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:9497/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1421975/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1123038/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:388197/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1500463/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1685148/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1008123/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:869393/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:1950424/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:186132/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:2629564/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:2620/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:2796940/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:2905063/69‑1 (MQ=255)

                                                 gatgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:2040184/69‑1 (MQ=255)

                                                  atgatATTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCg       <  1:38819/68‑1 (MQ=255)

                                                    gatATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTc     <  1:846994/68‑1 (MQ=255)

                                                    gatATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTc     <  1:417592/68‑1 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCaa   >  1:2499390/1‑68 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2275695/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2275804/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:1473002/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2408085/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:568338/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2576420/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:906288/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2029084/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:3043872/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:402797/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2731467/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:3378321/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:3356475/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2880955/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:1725236/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2987293/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:3102513/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:1721227/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATTGTCGCCATAACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2182247/1‑69 (MQ=255)

                                                      tatTGAAGCTCAGCTGATTGGTTCATAGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAc  >  1:2789836/1‑69 (MQ=255)

TGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATTAAGTAAAGCGTCAAC  >  minE/2950683‑2950805

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A