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	1,582,188	T→A	29.9%	A349A (GCA→GCT)	ligA ←	DNA ligase, NAD(+)‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,582,188	0	T	A	29.9%	95.9 / 49.4	80	A349A (GCA→GCT)	ligA	DNA ligase, NAD(+)‑dependent
Reads supporting (aligned to +/- strand): ref base T (13/43); new base A (22/2); total (35/45)
Fisher's exact test for biased strand distribution p-value = 9.24e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

CGTAAACCAAGACGTTCGATTTCATCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTC  >  minE/1582126‑1582253

cGTAAACCAAGACGTTCGATTTCATCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACa                                                             >  1:2167466/1‑69 (MQ=255)

cGTAAACCAAGACGTTCGATTTCATCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACa                                                             >  1:1417297/1‑69 (MQ=255)

cGTAAACCAAGACGTTCGATTTCATCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGAAACa                                                             >  1:1001810/1‑69 (MQ=255)

                        tCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAAc                                      <  1:1013036/68‑1 (MQ=255)

                        tCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAAc                                      <  1:2400471/68‑1 (MQ=255)

                        tCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAAc                                      <  1:2722131/68‑1 (MQ=255)

                        tCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAAc                                      <  1:3082744/68‑1 (MQ=255)

                        tCCGCATTGTGTAAGGTTGCGATACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAAc                                      <  1:637642/68‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:3379230/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:129965/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:1128290/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:900523/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:2359583/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:2305688/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:1640569/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:1821364/53‑1 (MQ=255)

                          cGCATTGTGTAAGGTTGCGTTACACACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:994402/53‑1 (MQ=255)

                           gCATTGTGTAAGGTTGCGTTACTCACCATCACGCCTGCAACATGGACAGGtt                                                   <  1:1549934/52‑1 (MQ=255)

                           gCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGtt                                                   <  1:379608/52‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:2619999/69‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:440979/69‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:3181124/69‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:146472/69‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:3021579/69‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:2548250/69‑1 (MQ=255)

                              ttGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTa                               <  1:678785/69‑1 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGTAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:3012179/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAgg                                                     >  1:2573754/1‑38 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:1441110/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:2730428/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:2831898/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:2523739/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:2260235/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:1051513/1‑68 (MQ=255)

                                       gTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:974907/1‑68 (MQ=255)

                                       gTTGAGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGcc                       >  1:1877196/1‑68 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:2984594/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:438976/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:2872905/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:3250951/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:3414893/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:13931/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:1019647/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:933728/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:2385946/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:2492369/69‑1 (MQ=255)

                                          gCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTa                   <  1:2138876/69‑1 (MQ=255)

                                              tACTCACCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTaa                              <  1:2769330/54‑1 (MQ=255)

                                              tACTCACCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTaa                              <  1:2302127/54‑1 (MQ=255)

                                                   aCCAACACGCCAGCATCATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:2202732/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCaa                                       >  1:833751/1‑40 (MQ=38)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAgga                                  >  1:402630/1‑44 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:78043/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1644792/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:390327/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:681775/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1052437/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:552911/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:495960/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:2424496/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1768031/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1884844/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1897208/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:2026947/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1543638/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:2363223/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:3231059/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:2485480/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:2690425/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:3008506/1‑45 (MQ=255)

                                                   aCCAACACGCCAGCAACATGGACAGGTTCCAGACGCGCAACAGGc                                  >  1:1408241/1‑45 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:2456011/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:645439/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:657877/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:280061/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:1504466/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:2837311/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:2088479/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:311079/69‑1 (MQ=255)

                                                           gCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTc  <  1:3206392/69‑1 (MQ=255)

CGTAAACCAAGACGTTCGATTTCATCCGCATTGTGTAAGGTTGCGTTACTCACCAGCACGCCTGCAACATGGACAGGTTCCAGACGCGCAACAGGCGTAATCGCGCCAGTACGCCCAACCTGAAACTC  >  minE/1582126‑1582253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A