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
A5 F1 I1 R1	19	34.1	2156969	96.4%	2079318	75.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,145,813	C→T	intergenic (+144/‑51)	dnaG → / → rpoD	DNA primase/RNA polymerase sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,145,813	0	C	T	94.1%	116.5 / ‑4.0	34	intergenic (+144/‑51)	dnaG/rpoD	DNA primase/RNA polymerase sigma factor
Reads supporting (aligned to +/- strand): ref base C (0/2); new base T (15/17); total (15/19)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCAC  >  REL606/3145742‑3145885

taAGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGt                                                                      >  1:668436/1‑76 (MQ=255)

 aaGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTc                                                                     >  1:68809/1‑76 (MQ=255)

 aaGTACGCCATCGTAATTATCGTTGGCGGTAAACAACCATTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTc                                                                     >  1:761451/1‑76 (MQ=255)

  aGTACGCCCTCGTAACTATCGTTGGCGGTAGACATGCGTTGGATTTCAACGTTAACGGCTGATGGACATTGGGTCa                                                                    <  1:970999/76‑1 (MQ=255)

          cTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCa                                                            >  2:503777/1‑76 (MQ=255)

              tAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAacac                                                        >  1:1035630/1‑76 (MQ=255)

                  tATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAAc                                                    <  1:463151/76‑1 (MQ=255)

                   aTCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAAcc                                                   >  1:323577/1‑76 (MQ=255)

                       ttGGCGGTAAACAACCGTTAGATTTCAGCGTTAACGGCTGAAGANCATCGGGTCTATCGCCCAACACCAACCTCAt                                               <  1:95132/76‑1 (MQ=255)

                             gTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATa                                         <  1:687061/76‑1 (MQ=255)

                              tcaacagcCGTTGGATTTCAGCNTTGACGGCTGNAGGACATTNGGTCAATCGCGCAACACCTACCNCATGAAATaa                                        <  2:939043/74‑1 (MQ=255)

                              tAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATaa                                        <  2:42163/76‑1 (MQ=255)

                              tAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATaa                                        >  2:223826/1‑76 (MQ=255)

                               aaaCAACAGTTGGATTTCAGCGTTAACGGCTGAAGGACATTCGGTCAATCGCCCAACACCAACATCATGAAATAAg                                       >  2:966760/1‑76 (MQ=255)

                                       gTTGGATTTCTGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATa                               <  1:601890/76‑1 (MQ=255)

                                       gTTGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATa                               <  1:309353/76‑1 (MQ=255)

                                        ttGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATAc                              <  2:794284/76‑1 (MQ=255)

                                        ntGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGAttc                              <  1:923111/75‑3 (MQ=255)

                                         tGGATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATAcc                             >  2:1068148/1‑76 (MQ=255)

                                          ggATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCg                            >  1:472916/1‑76 (MQ=255)

                                           gATTTCAGCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGt                           <  2:790392/76‑1 (MQ=255)

                                                cggCGTTNAAGGCTGAAGGACATTGGGTCAATCGCACAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTAt                      >  1:948666/3‑76 (MQ=255)

                                                  gCGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATgg                    >  2:437968/1‑76 (MQ=255)

                                                   cGTTAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGa                   <  1:310453/76‑1 (MQ=255)

                                                      tAACGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCa                >  2:1001566/1‑76 (MQ=255)

                                                       aaCGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTTTGGATACCGTCTTATGGAGCac               <  2:1050937/76‑2 (MQ=255)

                                                        aCGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaa              <  1:227883/76‑1 (MQ=255)

                                                        aCGGCTGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaa              <  2:878755/76‑1 (MQ=255)

                                                             tGAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg         >  1:670669/1‑76 (MQ=255)

                                                              gAAGGACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGc        <  2:611693/76‑1 (MQ=255)

                                                                  gACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTc    <  2:408841/76‑1 (MQ=255)

                                                                  gACATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTc    <  1:1035868/76‑1 (MQ=255)

                                                                  gACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTc    <  1:21439/76‑1 (MQ=255)

                                                                    cATTGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcac  >  2:57211/1‑76 (MQ=255)

TAAGTACGCCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCAC  >  REL606/3145742‑3145885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A