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
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,552,249	G→A	100%	intergenic (+119/+65)	torI → / ← dsdC	response regulator inhibitor for tor operon/DNA‑binding transcriptional dual regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,552,249	0	G	A	77.8%	130.9 / 34.3	72	intergenic (+119/+65)	torI/dsdC	response regulator inhibitor for tor operon/DNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand): ref base G (0/16); new base A (35/21); total (35/37)
Fisher's exact test for biased strand distribution p-value = 4.11e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch.

CCCTGCTGCTTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGTTTTAT  >  minE/1552182‑1552310

cccTGCTGCTTCAAGTAGATGTCTGCAGGTGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAAcc                                                            >  1:643968/1‑71 (MQ=255)

cccTGCTGCTTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAAcc                                                            >  1:3860894/1‑71 (MQ=255)

cccTGCTGCTTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAAc                                                             <  1:5077644/70‑1 (MQ=255)

        ctTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGtaaatt                                                     <  1:2844457/70‑1 (MQ=255)

        ctTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGtaaatt                                                     <  1:2560091/70‑1 (MQ=255)

        ctTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaatt                                                     <  1:94013/70‑1 (MQ=255)

        ctTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaatt                                                     <  1:353295/70‑1 (MQ=255)

              gTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCg                                              <  1:5457246/71‑1 (MQ=255)

               tAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCg                                              >  1:827243/1‑70 (MQ=255)

                 gATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAGAACCGTAAATTAAATTCGAAc                                           <  1:472317/71‑1 (MQ=255)

                   tGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTa                                         <  1:2041168/71‑1 (MQ=255)

                   tGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTa                                         <  1:2460505/71‑1 (MQ=255)

                   tGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTa                                         <  1:2453862/71‑1 (MQ=255)

                    gTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaattaaa                                                  <  1:1544813/61‑1 (MQ=255)

                    gTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAg                                        >  1:1998871/1‑71 (MQ=255)

                     tCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAg                                        >  1:2193488/1‑70 (MQ=255)

                         cAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCa                                      <  1:4012569/68‑1 (MQ=255)

                         cAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGta                                                         >  1:2805578/1‑49 (MQ=255)

                              gACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAAt                              <  1:2139922/71‑1 (MQ=255)

                              gACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGaa                               >  1:1044878/1‑70 (MQ=255)

                              gACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAAt                              <  1:316000/71‑1 (MQ=255)

                              gACACCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAAt                              <  1:4425711/71‑1 (MQ=255)

                               acacCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCg                                                           <  1:1817864/41‑1 (MQ=255)

                               acacCATCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATa                             <  1:2671832/71‑1 (MQ=255)

                                    aTCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaa                                                       >  1:3262800/1‑40 (MQ=255)

                                    aTCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaa                                                       >  1:2398290/1‑40 (MQ=255)

                                    aTCCTTGTGTTTATCCATAAAACCACATAAAAACCGTAAATTAAATTc                                               >  1:3874734/1‑48 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAGACCGtaaattaaa                                                  <  1:906970/44‑1 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAGACCGtaaattaaa                                                  <  1:2356231/44‑1 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaattaa                                                   >  1:2357453/1‑43 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaattaa                                                   >  1:2364124/1‑43 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCg                                 <  1:2373984/61‑1 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGca                        >  1:4418292/1‑70 (MQ=255)

                                     tCCTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGca                        >  1:1920351/1‑70 (MQ=255)

                                      ccTTGTGTTTATCCCTAAAACCACATAAAAACCGtaaa                                                       >  1:3081982/1‑38 (MQ=255)

                                      ccTTGTGTTTATCCCTAAAACCACATAAAAACCGtaa                                                        >  1:1365851/1‑37 (MQ=255)

                                      ccTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:4841250/1‑71 (MQ=255)

                                      ccTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:5025785/1‑71 (MQ=255)

                                       cTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCacac                     <  1:5690007/71‑1 (MQ=255)

                                       cTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCacac                     <  1:379662/71‑1 (MQ=255)

                                       cTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCg                                              <  1:594598/46‑1 (MQ=255)

                                       cTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCg                                              <  1:601524/46‑1 (MQ=255)

                                       cTTGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAg                                        >  1:1458843/1‑52 (MQ=255)

                                        ttGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCg                                              <  1:1044103/45‑1 (MQ=255)

                                        ttGTGTTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCacac                     >  1:844924/1‑70 (MQ=255)

                                          gtgtTTATCCCTAAAACCACATAAAAACCGTATATTAAATTCGAACTAGCAGGCCGAATAAGGCACAcc                    <  1:5334203/69‑1 (MQ=255)

                                           tgtTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAgg                 <  1:2774175/71‑1 (MQ=255)

                                           tgtTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGaa                                            >  1:3178307/1‑44 (MQ=255)

                                           tgtTTATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGaa                                            >  1:2020117/1‑44 (MQ=255)

                                             tttATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAgg                 <  1:3011098/69‑1 (MQ=255)

                                             tttATCCCTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCg                                 <  1:12381/53‑1 (MQ=255)

                                                  cccTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAAt                              <  1:213020/51‑1 (MQ=255)

                                                   ccTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGt          <  1:4065981/70‑1 (MQ=255)

                                                   ccTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGa                                <  1:3647562/48‑1 (MQ=255)

                                                   ccTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGa                                <  1:5512894/48‑1 (MQ=255)

                                                    cTAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGa                                <  1:2286845/47‑1 (MQ=255)

                                                     tAAAACCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGGGGt       >  1:402596/1‑71 (MQ=255)

                                                      aaaaCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGcc                                  >  1:1403328/1‑43 (MQ=255)

                                                      aaaaCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCg           >  1:4881652/1‑66 (MQ=255)

                                                      aaaaCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCg           >  1:1444597/1‑66 (MQ=255)

                                                       aaaCCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGttt     <  1:800798/71‑1 (MQ=255)

                                                       aaaCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGca                        >  1:99067/1‑52 (MQ=255)

                                                       aaaCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGttt     >  1:2520404/1‑71 (MQ=255)

                                                       aaaCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGt       <  1:1519964/69‑1 (MQ=255)

                                                         aCCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGTTTTa   <  1:1535236/71‑1 (MQ=255)

                                                         aCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGTTTTa   >  1:5079179/1‑71 (MQ=255)

                                                         aCCACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGTTTTa   >  1:1051355/1‑71 (MQ=255)

                                                          ccACATAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGTTTTAt  >  1:3252346/1‑71 (MQ=255)

                                                            acaTAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:5643809/1‑49 (MQ=255)

                                                            acaTAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:1032110/1‑49 (MQ=255)

                                                            acaTAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCacac                     >  1:1386247/1‑50 (MQ=255)

                                                            acaTAAAAACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAAc              >  1:3407548/1‑57 (MQ=255)

                                                                aaaaACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:5564990/1‑45 (MQ=255)

                                                                aaaaACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:5449094/1‑45 (MQ=255)

                                                                aaaaACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGcaca                      >  1:1333727/1‑45 (MQ=255)

CCCTGCTGCTTCAAGTAGATGTCTGCAGGGGACACCATCCTTGTGTTTATCCCTAAAACCACATAAAGACCGTAAATTAAATTCGAACTAGCAGGCCGAATAAGGCACACCAGGAACTCGTGGTTTTAT  >  minE/1552182‑1552310

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