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
A23 F148 I1 R1	14	45.7	1660340	90.3%	1499287	142.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	95.2%	119.5 / NA	42	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (21/19); minor base T (0/2); total (21/21)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCA  >  NC_000913/4184403‑4184677

tCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGGCATCGTACTGAACCAGc                                                                                                                                      >  2:146826/1‑143 (MQ=255)

       gTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGt                                                                                                                               >  1:405829/1‑143 (MQ=255)

                 gTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAAGTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                     <  1:49539/143‑1 (MQ=255)

                   agccAGCCTGGCGACAACATGGCCGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                   <  1:242638/141‑1 (MQ=255)

                    tCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGGGTACCGTCCCggaag                                                                                                                  >  2:308630/1‑139 (MQ=255)

                           tGGTGAGAAGATGGCAGGTCGGCACGGTAAGAAGGGTGTAAGGTATAAGAGCGACCCGATCGAAGATATGCCTTACGAGGAAAACGGTACGCCGGTAGACATCGGACTGAACCAGCTGGGCGTACCGCCTCGTGTGAATATCg                                                                                                           <  2:729600/143‑1 (MQ=255)

                           tGGGGACAAGATGGTAGGTCCTTACTGTAACATGTGTGTAATTTCTAATATCAACCCTATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                           <  1:782992/143‑1 (MQ=255)

                               gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                       >  1:313391/1‑143 (MQ=255)

                                 ccaGATGGCAGGGCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGa                                                                                                     <  2:28110/141‑1 (MQ=255)

                                   aGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGACCATCGGTCAGagc                                                                                                   >  1:79582/1‑141 (MQ=255)

                                     aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGTCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                                 <  1:35536/143‑1 (MQ=255)

                                      tGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCACCCCGCTGGTAACGTGGCGTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                <  1:187151/143‑1 (MQ=255)

                                         cAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATTAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaa                                                                                             <  1:823186/143‑1 (MQ=255)

                                          aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCGACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                            <  2:236151/143‑1 (MQ=255)

                                          aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                            >  1:790519/1‑143 (MQ=255)

                                          aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGCCAGATCCTCaaaa                                                                                            >  2:744008/1‑143 (MQ=255)

                                               gtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAc                                                                                       >  1:449565/1‑143 (MQ=255)

                                                tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAGACCCAcc                                                                                      >  1:181266/1‑143 (MQ=255)

                                                tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcc                                                                                      >  1:695407/1‑143 (MQ=255)

                                                         cAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCGTACGATGAAAACGGTACGCCGGTAGACCTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                             <  1:359833/143‑1 (MQ=255)

                                                            gggTGTAATTTCTAAGATCAACCCGATCGGCGTTCTGCCGTACGAGGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTg                                                                          <  1:781738/143‑1 (MQ=255)

                                                                 tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGAACTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGGCAGACGCTCGCAACCCACCTGGGGATGGCTGCggca                                                                     >  2:511477/1‑140 (MQ=255)

                                                                 tAAGTTTTATGATCGACCCGCTCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGTGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAATCCTCCTGGGTATGGCTGCGaaa                                                                     <  2:20805/143‑1 (MQ=255)

                                                                  actttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                    <  2:659130/141‑1 (MQ=255)

                                                                      tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTAt                                                                >  1:366258/1‑143 (MQ=255)

                                                                       cTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCTTCTCGTATGAACATAGGTCAGATCCTCGAAACACACCCGGGCATCGCAGCGGAAgggaag                                                               >  2:621721/1‑139 (MQ=255)

                                                                            agcAACCCGATCGAAGATATGCCTTACGACGGAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                          <  2:462192/141‑1 (MQ=255)

                                                                             tCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGGATGAACATCGGTCAGATCCCCGAAACCCGTCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                         <  1:569341/143‑1 (MQ=255)

                                                                                  ccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTAGCGGCGACAAGAt                                                    >  1:707272/1‑143 (MQ=255)

                                                                                                  cTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                    >  1:608674/1‑143 (MQ=255)

                                                                                                      cGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTATGGCAGCGCGAGGGATCGGCGACAAGCTCCAAGCCAAGCGCAAAcagc                                >  2:391913/1‑143 (MQ=255)

                                                                                                      cGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaaatgc                                >  2:392790/1‑139 (MQ=255)

                                                                                                            gcgcGGTACGCCGGTGGAGATCGTACTGGACGAGCTGGGCGTGCCGTCTCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaag                          <  2:289989/140‑1 (MQ=255)

                                                                                                            aaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACCAGATCAACGCCATGCTGACACAGCAGCaag                          >  1:212202/1‑143 (MQ=255)

                                                                                                             aaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaaga                         >  1:110152/1‑143 (MQ=255)

                                                                                                              gcGGTCCGTCGGTCGACACCGGACTGTACCTGCTGGTCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGACACCACCCTGGGTATGTCTGCGAAAGGTATCGTCGACAAGATCAACGCCATGCTGAAACAGCAGCaagaa                        <  2:206955/142‑1 (MQ=255)

                                                                                                                     gCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                 <  1:759322/143‑1 (MQ=255)

                                                                                                                       cGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATACTCGAAACCGACCTGGGTATGGCTGCGAAAGGTACCGGCGACAAGATCAACGCCATGCTGAAACAGCCGCAAGAAGGCGCGaaa               >  2:424375/1‑143 (MQ=255)

                                                                                                                            gACATCGTACTGAGCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGCAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcg          <  1:257117/143‑1 (MQ=255)

                                                                                                                                 cGTACTGAACCTGCGGCGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt     <  2:9753/143‑1 (MQ=255)

                                                                                                                                 cGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt     <  1:378467/143‑1 (MQ=255)

                                                                                                                                    aCTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGACTTCa  >  1:208295/1‑143 (MQ=255)

TCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCA  >  NC_000913/4184403‑4184677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A