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 F8 I0 R2	296	77.6	4260404	88.1%	3753415	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,747,876	G→A	26.2%	S44L (TCA→TTA)	yfiE ←	predicted DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,747,876	0	G	A	26.2%	109.7 / 39.7	61	S44L (TCA→TTA)	yfiE	predicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (19/26); new base A (12/4); total (31/30)
Fisher's exact test for biased strand distribution p-value = 4.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCAACTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTACAGCACAATTTTTGC  >  minE/1747814‑1747941

gcaACTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTcc                                                           <  1:1566472/71‑1 (MQ=255)

gcaACTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTcc                                                           <  1:1562609/71‑1 (MQ=255)

  aaCTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTaaa                                                                 <  1:2125771/63‑1 (MQ=255)

    cTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCt                                                       >  1:85650/1‑71 (MQ=255)

    cTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCt                                                       >  1:2199104/1‑71 (MQ=255)

      tttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTc                                                      >  1:2079525/1‑70 (MQ=255)

      tttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTc                                                      >  1:4146769/1‑70 (MQ=255)

       ttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTc                                                      >  1:1023725/1‑69 (MQ=255)

       ttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTc                                                      >  1:1630154/1‑69 (MQ=255)

       ttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTc                                                      >  1:4019832/1‑69 (MQ=255)

       ttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTc                                                      >  1:593259/1‑69 (MQ=255)

       ttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTc                                                      >  1:3716348/1‑69 (MQ=255)

       ttttCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTc                                                      >  1:3591287/1‑69 (MQ=255)

                    gTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAatat                                        >  1:4136570/1‑70 (MQ=255)

                    gTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTCa                                                     <  1:1615478/57‑1 (MQ=255)

                    gTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTCa                                                     <  1:232114/57‑1 (MQ=255)

                     tAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATg                                       >  1:2639351/1‑70 (MQ=255)

                     tAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATg                                       >  1:2671165/1‑70 (MQ=255)

                     tAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATg                                       >  1:1066526/1‑70 (MQ=255)

                       aGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTCAAGCTGCTGAATATGaa                                     >  1:2200539/1‑70 (MQ=255)

                       aGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTCAAGCTGCTGAATATGaa                                     >  1:3202941/1‑70 (MQ=255)

                       aGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTAAAAACTCCTGCTCAAGCTGCTGAATATGaa                                     >  1:1159041/1‑70 (MQ=255)

                            caTCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTc                                <  1:1490982/70‑1 (MQ=255)

                             aTCCGTCGGCCAATTTTCTCAAATAACTGGACTGaa                                                                 <  1:2107260/36‑1 (MQ=255)

                             aTCCGTCGGCCAATTTTCTCAAATAACTGGACTGaa                                                                 <  1:2375018/36‑1 (MQ=255)

                             aTCCGTCGGCCAATTTTCTCAAATAACTGGACTGaa                                                                 <  1:3956817/36‑1 (MQ=255)

                             aTCCGTCGGCCAATTTTCTCAAATAACTGGACTGaa                                                                 <  1:3407432/36‑1 (MQ=255)

                              tCCGTCGGCCAATTTTCTCAAATAACTGGACTGaa                                                                 <  1:4023709/35‑1 (MQ=255)

                              tCCGTCGGCCAATTTTCTCAAATAACTGGACTGGAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCAcc                             >  1:2757661/1‑71 (MQ=255)

                              tCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCAcc                             >  1:3862636/1‑71 (MQ=255)

                              tCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCAcc                             >  1:3758579/1‑71 (MQ=255)

                              tCCGTCGGCCAATTTTCTCAAATAACAGGACTGaaaa                                                               >  1:1720287/1‑37 (MQ=255)

                                cGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGt                           >  1:3972795/1‑71 (MQ=255)

                                 gTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTc                          <  1:2720507/71‑1 (MQ=255)

                                  tCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGaa                                     <  1:3507795/59‑1 (MQ=255)

                                  tCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCg                         <  1:322633/71‑1 (MQ=255)

                                  tCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCg                         <  1:327645/71‑1 (MQ=255)

                                      ccAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtg                     <  1:935540/71‑1 (MQ=255)

                                      ccAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtg                     <  1:4231648/71‑1 (MQ=255)

                                        aaTTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:3583042/71‑1 (MQ=255)

                                        aaTTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:2187576/71‑1 (MQ=255)

                                         aTTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:3361362/70‑1 (MQ=255)

                                         aTTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:2003396/70‑1 (MQ=255)

                                         aTTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:4187869/70‑1 (MQ=255)

                                          ttttCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTa                 >  1:2942267/1‑71 (MQ=255)

                                           tttCTCAAATAACTGGACTAAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTa                 >  1:2710059/1‑70 (MQ=255)

                                            ttCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:1242188/67‑1 (MQ=255)

                                            ttCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:2844874/67‑1 (MQ=255)

                                            ttCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTa                 >  1:3851266/1‑69 (MQ=255)

                                              ctcAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGa                                      >  1:130127/1‑46 (MQ=255)

                                              ctcAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGt                                 >  1:617569/1‑51 (MQ=255)

                                              ctcAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGt                                 >  1:1971556/1‑51 (MQ=255)

                                               tcAAATAACTGGACTAAAAACTCCTGCTCAAGCTGCTGaa                                           <  1:1156842/40‑1 (MQ=255)

                                               tcAAATAACTGGACTAAAAACTCCTGCTCAAGCTGCTGaa                                           <  1:1292853/40‑1 (MQ=255)

                                                 aaataaatGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTACAGcac           >  1:6594/1‑70 (MQ=255)

                                                 aaaTAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATGTGAAAAGTCACCGTc                          <  1:1430970/55‑1 (MQ=255)

                                                 aaaTAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTc                          <  1:799501/55‑1 (MQ=255)

                                                 aaaTAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTACAGcac           >  1:2125335/1‑70 (MQ=255)

                                                   aTAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGt                                 <  1:2999274/46‑1 (MQ=255)

                                                          gACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTACAGCACAATTTTTGc  >  1:3111224/1‑70 (MQ=255)

                                                             tGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:4152240/50‑1 (MQ=255)

                                                             tGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:2624720/50‑1 (MQ=255)

                                                              gAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATtgtg                   <  1:48626/49‑1 (MQ=255)

GCAACTTTTTTCCTTCGCGGGTAAGGCACATCCGTCGGCCAATTTTCTCAAATAACTGGACTGAAAACTCCTGCTCAAGCTGCTGAATATGAAAAGTCACCGTCGATTGTGTACAGCACAATTTTTGC  >  minE/1747814‑1747941

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