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
A15 F59 I0 R1	41	74.1	1560052	97.4%	1519490	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,440,007	Δ1 bp	100%	coding (34/201 nt)	cspA ←	cold shock protein CspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,440,007	0	C	.	97.8%	205.4 / ‑3.3	46	coding (34/201 nt)	cspA	cold shock protein CspA
Reads supporting (aligned to +/- strand): ref base C (1/0); new base . (28/17); total (29/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT  >  CP000730/1439875‑1440140

ggTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTaaa                                                                                                                              <  1:611391/141‑1 (MQ=255)

             tactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTa                                                                                                                 >  1:403008/1‑141 (MQ=255)

                  cAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTg                                                                                                            >  1:91474/1‑141 (MQ=255)

                   aaaCTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGt                                                                                                           >  1:287199/1‑141 (MQ=255)

                       tCAACCGCCTGTCCTCCTTTCAATGATTTTCAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCTATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCa                                                                                                       <  1:399830/141‑1 (MQ=255)

                       tCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCa                                                                                                       <  1:436237/141‑1 (MQ=255)

                          aCAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATaa                                                                                                    >  1:104477/1‑141 (MQ=255)

                           cAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAAt                                                                                                   >  1:41231/1‑141 (MQ=255)

                                  aCCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTCAACCACTTAACTGTACCTTGTTTCATAATCTGAAAc                                                                                            <  1:405263/141‑1 (MQ=255)

                                          ctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTTTCCTTCAACTTCGTTAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATTTGTATCCTCCAAGa                                                                                    >  2:611120/1‑141 (MQ=255)

                                           tAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGaa                                                                                   >  2:328716/1‑140 (MQ=255)

                                           tAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAc                                                                                   <  1:756185/141‑1 (MQ=255)

                                            aaTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACTTCCAAGACt                                                                                  >  1:644834/1‑141 (MQ=255)

                                             aTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCAATAAAACGTATAACTGGACCTTGTTTCATAATCTGAAACCTCCGAGACTa                                                                                 >  1:525397/1‑141 (MQ=255)

                                                       aCCATCTTGGTTGATTGCTGAAAAATGTACGACTACGTCATTTTCTCCTTCAACTTCGATAAAACCGAATCCCTTTT‑AGCGTTAAACCATTCAACTGTCCCTTGTTTCATCATATGAAACCCACAAGACTAAAcatcattc                                                                       >  2:651651/1‑141 (MQ=255)

                                                       aCCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCAGAATCCTTTAT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc                                                                       >  2:83070/1‑141 (MQ=255)

                                                            cTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAatat                                                                  <  2:104477/141‑1 (MQ=255)

                                                              tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGCCTAAAATTCATTCAATATGc                                                                >  1:192466/1‑141 (MQ=255)

                                                                 ttAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTa                                                             >  1:719108/1‑141 (MQ=255)

                                                                   aaTTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAtt                                                           >  1:354463/1‑141 (MQ=255)

                                                                   aaTTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAtt                                                           >  2:527266/1‑141 (MQ=255)

                                                                    aTTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTc                                                          >  2:302421/1‑141 (MQ=255)

                                                                       gCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCa                                                       >  1:748123/1‑141 (MQ=255)

                                                                          gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                    >  1:216279/1‑141 (MQ=255)

                                                                             aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAc                                                 >  2:145648/1‑141 (MQ=255)

                                                                              attGTACGACTACGTCAGTGTCTCATTCAACTTCGTTAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACa                                                <  1:420215/139‑1 (MQ=255)

                                                                               aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaa                                               <  2:663140/141‑1 (MQ=255)

                                                                                 gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGCATCC‑TTTTCAGCGTTAAACCATTTAACTGTACCTTGCTTCATAATCTTAAACCTCCAAGACTAAAATTCACTCAATATTCTTATTCGCATATCACataa                                             >  1:407798/1‑141 (MQ=255)

                                                                                    cGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAAt                                          >  1:497923/1‑141 (MQ=255)

                                                                                         tcGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAATCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACGAAAAATACATg                                     <  2:231209/140‑1 (MQ=255)

                                                                                         atctCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGCTAAACCATTTAACTGTACCTTGGTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCGTATTCGCATATTACAAAAAATACATg                                     <  2:78349/138‑1 (MQ=255)

                                                                                         aCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                     <  2:265631/141‑1 (MQ=255)

                                                                                            tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCaa                                  <  2:231590/141‑1 (MQ=255)

                                                                                            tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCaa                                  <  1:710969/141‑1 (MQ=255)

                                                                                               tgttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAAtt                               <  1:437307/139‑1 (MQ=255)

                                                                                                 ttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTc                             >  2:585452/1‑141 (MQ=255)

                                                                                                    tcCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACt                          >  1:689868/1‑141 (MQ=255)

                                                                                                     ccTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACAATTTAACTGTACCTTGTTTCATAATCTGAAACCTCGAAGACTAAAATTCATTCAATATGCTTATTCGCATATTGAAAAAAATACATGCAAAtttacatt                         >  1:111482/1‑136 (MQ=255)

                                                                                                           aCTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAatat                   <  1:607515/141‑1 (MQ=255)

                                                                                                              tCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                <  1:741135/141‑1 (MQ=255)

                                                                                                                    aaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAGTTTCACTCATATATTCTTTGCaa          >  1:57478/1‑141 (MQ=255)

                                                                                                                     aGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat         >  2:629592/1‑141 (MQ=255)

                                                                                                                     aGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat         >  2:338824/1‑141 (MQ=255)

                                                                                                                      gCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCCTAATCTGAAACGTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACATCAAATACATGCAAATTTCACTCAAATATTTTTTCCAatt        >  2:607248/1‑140 (MQ=255)

                                                                                                                          aaTCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGa    >  1:116818/1‑141 (MQ=255)

                                                                                                                            tCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat  <  2:341537/141‑1 (MQ=255)

GGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT  >  CP000730/1439875‑1440140

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A