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
A20 F53 I6 R4 121 75.7 2723416 94.9% 2584521 126.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,813,837 T→C L304P (CTT→CCT)  U712_19660 → Peptidase T

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,813,8370TC96.2% 185.1 / ‑3.3 53L304P (CTT→CCT) U712_19660Peptidase T
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (24/27);  total (25/28)
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

TATGAAGGCTTCTACCACCTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACTTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGAAAACCTCGGCA  >  CP006881/3813704‑3813965
                                                                                                                                     |                                                                                                                                
tATGAAGGCTTCTACCACCTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCaa                                                                                                                              >  2:229355/1‑138 (MQ=255)
 aTGAAGGCTTCTACCACCTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCaaa                                                                                                                             <  8:47838/138‑1 (MQ=255)
         ttCTACCACCTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACg                                                                                                                    >  4:300438/1‑139 (MQ=255)
              ccaccTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACggg                                                                                                                  <  4:150105/136‑1 (MQ=255)
                 ccTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCa                                                                                                                <  7:285967/135‑1 (MQ=255)
                 ccTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCa                                                                                                                >  8:285967/1‑135 (MQ=255)
                 ccTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGAc                                                                                                            >  2:20129/1‑139 (MQ=255)
                  ctgctgTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGAcc                                                                                                           >  7:321973/1‑139 (MQ=255)
                     ctgTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGa                                                                                                        >  6:154405/1‑139 (MQ=255)
                      tgTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGAt                                                                                                       >  4:39611/1‑139 (MQ=255)
                               aaGGAGACTTATAGTAAACAATGCTCCACTACATTATAAGAGAGTTTGACAAAGAGAATTTCCAAAAAATAAAAGAAAAAATTAAGCGTGCCGTTGAATAACCTCAAAACGAATACGGGCAAGACCGTATTctgctgta                                                                                              <  4:312110/139‑3 (MQ=255)
                               aaGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGa                                                                                              >  4:285115/1‑139 (MQ=255)
                                       gTAGAGGAAACATAGCTACACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGATGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACg                                                                                      <  1:233514/139‑1 (MQ=255)
                                       gTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACg                                                                                      <  7:75438/139‑1 (MQ=255)
                                         atagcaaaCAAAGCTCCACTACATTATCACAGACTTTGACAAACAGAATTACCAAAACCGAAAAGAAACAATGAAGCGGGCCGTGCAAGAACCTCAAACCGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  2:115676/134‑1 (MQ=255)
                                         agagGAACCAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATATCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTAGAAGAACCTCAACACGAATACTGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  5:304641/139‑1 (MQ=255)
                                         agagGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTCCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    >  4:45932/1‑139 (MQ=255)
                                         agagCAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  5:253677/139‑1 (MQ=255)
                                          gagGAAACCAAGCTCCACTACATTATCAGAGACTTTGAAAAAGAGAATATCCAAAACAGAAAAGAAACATTGAAGCGTGCCGTTTAAGAACCTCAAAACGAATACGGTCAAGACCGGATTCTGCTGGATATGAAGGAc                                                                                    <  5:161262/138‑1 (MQ=255)
                                          gagGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  7:68779/138‑1 (MQ=255)
                                          gagGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  6:45140/138‑1 (MQ=255)
                                          gagGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  6:125740/138‑1 (MQ=255)
                                          gagGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  8:117755/138‑1 (MQ=255)
                                             gAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACTTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCaa                                                                                 >  3:102254/1‑138 (MQ=255)
                                             gAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCaa                                                                                 >  4:160640/1‑138 (MQ=255)
                                             gAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCaa                                                                                 >  8:156057/1‑138 (MQ=255)
                                               aaCAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAAtac                                                                              >  4:270088/1‑139 (MQ=255)
                                               aaCAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAAtac                                                                              <  8:321973/139‑1 (MQ=255)
                                               aaCAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAAtac                                                                              <  1:199665/139‑1 (MQ=255)
                                                 cAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAAtacta                                                                            <  6:166436/139‑1 (MQ=255)
                                                     gCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTacaa                                                                         >  3:250337/1‑138 (MQ=255)
                                                         cACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGa                                                                                         <  6:127089/118‑1 (MQ=255)
                                                         cACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGa                                                                                         >  5:127089/1‑118 (MQ=255)
                                                             aCATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATgagaga                                                                <  3:270088/139‑1 (MQ=255)
                                                              cATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACTTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATgagaga                                                                <  4:102254/138‑1 (MQ=255)
                                                                      gagaCTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTg                                                        >  3:89887/1‑138 (MQ=255)
                                                                        gaCTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAAc                                                     >  1:320078/1‑139 (MQ=255)
                                                                        gaCTTTGACAAAGAGAATTCCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAAc                                                     <  3:45932/139‑1 (MQ=255)
                                                                           tttGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTg                                                  >  4:158641/1‑139 (MQ=255)
                                                                             tGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGt                                                 >  1:269773/1‑138 (MQ=255)
                                                                             tGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCAGCTGGAAAAGAACGACCAATACTACAACATGAGAGAGAAAAATGAACCTGt                                                 >  7:210627/1‑138 (MQ=255)
                                                                                 aaaGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCg                                            <  3:158641/139‑1 (MQ=255)
                                                                                   agagAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    <  3:37510/97‑1 (MQ=255)
                                                                                   agagAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGAc                                                                                    >  4:37510/1‑97 (MQ=255)
                                                                                   agagAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGaa                                          <  4:250337/139‑1 (MQ=255)
                                                                                         tttCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGt                                     >  2:59707/1‑138 (MQ=255)
                                                                                                     aaaagaaaCAATGAAGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCcaag                        >  2:96675/1‑139 (MQ=255)
                                                                                                               aTGAAGCGTGCCGTGGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATgg              <  2:269773/139‑1 (MQ=255)
                                                                                                                  aaGCGTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGaa            <  4:11498/138‑1 (MQ=255)
                                                                                                                      gTGCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGAAAACCt       <  1:20129/139‑1 (MQ=255)
                                                                                                                        gCCGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGAAAACCTCg     >  1:278644/1‑139 (MQ=255)
                                                                                                                          cGTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGAAAACCTCGGc   >  4:320928/1‑139 (MQ=255)
                                                                                                                           gTTGAAGAACCTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGAAAACCTCGGCa  <  3:300438/139‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                
TATGAAGGCTTCTACCACCTGCTGTCGATTCAAGGAGACGTAGAGGAAACAAAGCTCCACTACATTATCAGAGACTTTGACAAAGAGAATTTCCAAAACAGAAAAGAAACAATGAAGCGTGCCGTTGAAGAACTTCAAAACGAATACGGGCAAGACCGGATTCTGCTGGATATGAACGACCAATACTACAACATGAGAGAGAAAATTGAACCTGTCATCGAAATCGTCAACATTGCCAAGCAAGCGATGGAAAACCTCGGCA  >  CP006881/3813704‑3813965

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A