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
A12 F1 I1 R1	18	38.4	2430560	95.7%	2326045	75.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,145,984	A→T	I41F (ATC→TTC)	rpoD →	RNA polymerase sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,145,984	0	A	T	96.3%	95.4 / NA	27	I41F (ATC→TTC)	rpoD	RNA polymerase sigma factor
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (14/12); minor base G (0/1); total (14/13)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATC  >  REL606/3145911‑3146056

tAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCagatcagttc                                                                        <  1:1149492/76‑1 (MQ=255)

 aaGGAACAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCg                                                                       >  1:1139204/1‑76 (MQ=255)

     aGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGa                                                                   <  1:981656/76‑1 (MQ=255)

      gCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGAc                                                                  <  1:660304/76‑1 (MQ=255)

       cAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGAca                                                                 <  1:1154238/76‑1 (MQ=255)

            cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACatcatc                                                            >  2:897824/1‑76 (MQ=255)

              aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTCCGAAGACATCATCCa                                                          <  1:110340/76‑1 (MQ=255)

                  gACCTATGCCGAGGTCAATGACCTTATGCCGGAAGATATNGTCGAATCAGATCAGNTCGAAGTCATCATCCaaacg                                                      >  2:1197837/1‑74 (MQ=255)

                  gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAGGACATCATCCAAATg                                                      >  1:7881/1‑76 (MQ=255)

                  gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATg                                                      >  1:589437/1‑76 (MQ=255)

                         gCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACg                                               <  1:574708/76‑1 (MQ=255)

                            gAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACa                                            >  1:613221/1‑76 (MQ=255)

                              ggTCAATGACCATCTGCGGTAAGATATCGTCGATTCAGATCAGTTCGAAGATATCATCCAAATGATCAACGACATg                                          <  1:55055/76‑1 (MQ=255)

                                    ttaCCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCAtt                                    <  2:1093761/74‑1 (MQ=255)

                                    tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCAtt                                    >  2:60980/1‑76 (MQ=255)

                                     gACCATCTGCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTc                                   <  2:294036/76‑1 (MQ=255)

                                      aCCATCTGNCGGGAGATATCGTCGTTTGAGATCTGGTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCa                                  <  2:202583/76‑1 (MQ=255)

                                          tCTGCCGGAAGATATCGACGATGCAGATCAGTTCGAAGACATCATCCAAATGATCCACGACATGGGCATTCAGGTg                              <  1:55966/76‑1 (MQ=255)

                                             gCCGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATg                           >  2:639356/1‑76 (MQ=255)

                                              ccGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATgg                          >  1:782006/1‑76 (MQ=255)

                                               cGGAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGga                         >  2:1003205/1‑76 (MQ=255)

                                                ggAAGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa                        >  2:1132719/1‑76 (MQ=255)

                                                  aaGATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaaga                      <  2:756585/76‑1 (MQ=255)

                                                    gATATCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGTTGATGGaagaag                    <  2:48148/76‑1 (MQ=255)

                                                     atatCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATNGAAGAAGc                   <  1:1167822/76‑1 (MQ=255)

                                                      tatCGTCGATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCa                  >  1:976058/1‑76 (MQ=255)

                                                         cgtcgATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg               >  1:575462/1‑76 (MQ=255)

                                                         cgtcgATTCAGAGCACTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGNTGGAAGAAGCACCg               >  1:1038328/1‑76 (MQ=255)

                                                            cgATTCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAt            >  2:165716/1‑76 (MQ=255)

                                                               ttCAGATCAGTTCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGcc         >  2:379855/1‑76 (MQ=255)

                                                                    atcagttcGAAGACATCATCCAAATGATCAACGACATNGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatga    >  1:1185766/1‑76 (MQ=255)

                                                                    atcagttcGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatga    <  2:1112352/76‑1 (MQ=255)

                                                                     tcagttcGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACAGGATGCCgatgat   >  2:555448/1‑76 (MQ=255)

                                                                      cagttcGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATc  >  1:735573/1‑76 (MQ=255)

TAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATC  >  REL606/3145911‑3146056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A