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	2,405,511	A→G	39.2%	I650I (ATT→ATC)	cyaA ←	adenylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,405,511	0	A	G	39.2%	20.0 / 32.6	51	I650I (ATT→ATC)	cyaA	adenylate cyclase
Reads supporting (aligned to +/- strand): ref base A (15/16); new base G (8/12); total (23/28)
Fisher's exact test for biased strand distribution p-value = 5.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGACGCAATTCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTG  >  minE/2405463‑2405576

aaGACGCAATTCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCt                                                <  1:2993142/68‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:708463/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:1111591/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:3335254/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:2846674/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:355186/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:1391511/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:1422025/69‑1 (MQ=255)

          tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                     <  1:1538852/69‑1 (MQ=255)

             aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                   <  1:1323698/68‑1 (MQ=255)

             aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                   <  1:3290710/68‑1 (MQ=255)

             aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                   <  1:3431183/68‑1 (MQ=255)

             aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                   <  1:2775273/68‑1 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGAc                                >  1:2162810/1‑68 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:1578578/1‑69 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:2413519/1‑69 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:2457303/1‑69 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:173397/1‑69 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:378332/1‑69 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:436693/1‑69 (MQ=255)

                cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                               >  1:1074664/1‑69 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:3074198/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:825665/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:296929/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:471675/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:546030/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:1110951/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:223546/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:210619/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:1716287/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:1680263/68‑1 (MQ=255)

                       aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGAGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:2767666/68‑1 (MQ=255)

                         aCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                         <  1:670601/66‑1 (MQ=255)

                         aCCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTa                      <  1:3240112/69‑1 (MQ=255)

                             gTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTg                  >  1:533604/1‑69 (MQ=255)

                             gTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTg                  >  1:522111/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:3435593/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:1122169/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:467959/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:1205545/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:364318/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:2719789/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg               >  1:3345405/1‑69 (MQ=255)

                                gctgcACGCGAGTACGGATTAAGCCGCG‑‑GATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCGGt             >  1:1119027/1‑69 (MQ=255)

                                gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg               >  1:1559663/1‑69 (MQ=255)

                                gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg               >  1:1585904/1‑69 (MQ=255)

                                gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg               >  1:1801266/1‑69 (MQ=255)

                                gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg               >  1:2662520/1‑69 (MQ=255)

                                            tACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCt   <  1:1291375/69‑1 (MQ=255)

                                            tACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCt   <  1:1056814/69‑1 (MQ=255)

                                             aCGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTg  >  1:2072314/1‑69 (MQ=255)

AAGACGCAATTCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTG  >  minE/2405463‑2405576

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A